/var/spool/slurm/d/job6319943/slurm_script: line 14: activate: No such file or directory N E X T F L O W ~ version 20.10.0 Launching `nextNEOpi.nf` [thirsty_caravaggio] - revision: d919f63148 NEXTFLOW ~ version 20.10.0 5430 ------------------------------------------------------------------------- Nextfow NeoAntigen Prediction Pipeline - nextNEOpi ------------------------------------------------------------------------- Features: - somatic variants from tumor + matched normal samples - CNV analysis - tumor muational burden - class I and class II HLA typing - gene fusion peptide prediction using RNAseq data - peptide MHC binding perdiction - clonality of neoantigens - expression of neoantigens ------------------------------------------------------------------------- C O N F I G U R A T I O N Command Line: nextflow run nextNEOpi.nf --batchFile batchFile_subsample.csv -config conf/params.config --outputDir nextNeoPi_results --trim_adapters true --trim_adapters_RNAseq true --use_NetChop false --accept_license --resume -profile singularity,cluster Working Directory: /data/kryan/neoant/nextNEOpi Output Directory: nextNeoPi_results I N P U T batch file: batchFile_subsample.csv Please check --help for further instruction ------------------------------------------------------------------------- WARN: I have read and accept the licence terms tmpDir: /tmp/kryan/nextNEOpi Pipeline Name : icbi/nextNEOpi Pipeline Version : 1.0 Batch file : batchFile_subsample.csv Read length : 150 Exome capture kit : sureSelectV6 Fasta Ref : /data/kryan/neoant/nextNEOpi/resources/references/hg38/gdc/GRCh38.d1.vd1/fasta/GRCh38.d1.vd1.fa MillsGold : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf hcSNPS1000G : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz HapMap : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/hapmap_3.3.hg38.vcf.gz Cosmic : /data/kryan/neoant/nextNEOpi/resources/databases/cosmic/hg38/v84/CosmicCodingMuts.hg38.v84.vcf DBSNP : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.dbsnp138.vcf GnomAD : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/GetPileupSummaries/small_exac_common_3.hg38.vcf GnomADfull : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/gnomAD/af-only-gnomad.hg38.vcf.gz KnownIndels : /data/kryan/neoant/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.known_indels.vcf BlastDB : /data/kryan/neoant/nextNEOpi/resources/references/blast/ priority variant Caller : M2 Mutect 1 and 2 minAD : 5 VarScan min_cov : 10 VarScan min_cov_tumor : 10 VarScan min_cov_normal : 10 VarScan min_freq_for_hom : 0.75 VarScan somatic_pvalue : 0.99 VarScan somatic_somaticpvalue : 0.05 VarScan strand_filter : 1 VarScan processSomatic_pvalue : 0.05 VarScan max_normal_freq : 0.05 VarScan min_tumor_freq : 0.1 VarScan min_map_q : 10 VarScan min_base_q : 20 VEP assembly : GRCh38 VEP species : homo_sapiens VEP options : --everything Number of scatters : 40 Output dir : nextNeoPi_results Working dir : /data/kryan/neoant/nextNEOpi/work TMP dir : /tmp/kryan/nextNEOpi Current home : /home/kryan Current user : kryan Current path : /data/kryan/neoant/nextNEOpi JAVA_Xmx : -Xmx64G Picard maxRecordsInRam : 4194304 Script dir : /data/kryan/neoant/nextNEOpi Config Profile : singularity,cluster E-mail Address : k.ryan45@nuigalway.ie ------------------------------------------------------------------------- WARNING: sample1 sex not specified will infer from data WARNING: sample1 sex not specified will infer from data WARNING: sample1 sex not specified will infer from data Found /data/kryan/sw/hlahd.1.4.0/bin/hlahd.sh at: /data/kryan/sw/hlahd.1.4.0/bin/hlahd.sh [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [- ] process > BaitsBedToIntervalList [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC [ 0%] 0 of 3 [- ] process > fastp [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - executor > slurm (3) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [fa/ac56ba] process > FastQC (sample1 : tumor_RNA) [ 0%] 0 of 3 [- ] process > fastp [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - INFO: Mutect1 not available, skipping.... executor > slurm (8) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [ 0%] 0 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [- ] process > make_CNVkit_access_file [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - INFO: Mutect1 not available, skipping.... executor > slurm (11) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [ 0%] 0 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [- ] process > mixcr - [- ] process > collectSampleInfo - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (11) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [ 0%] 0 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [- ] process > mixcr - [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (11) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [ 0%] 0 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [- ] process > mixcr - [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (11) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [ 0%] 0 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [- ] process > mixcr - [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (11) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [55/04f43c] process > FastQC (sample1 : normal_DNA) [ 33%] 1 of 3 [3a/8a5824] process > fastp (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > FastQC_trimmed - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [- ] process > mixcr - [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (14) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [a5/92bbd5] process > FastQC_trimmed (sample1 : t... [ 0%] 0 of 3 [- ] process > make_uBAM [ 0%] 0 of 2 [- ] process > Bwa [ 0%] 0 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 1 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [eb/4f3d7b] process > mixcr (sample1 : tumor_RNA) [ 0%] 0 of 3 [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (19) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [56/87e0e3] process > FastQC_trimmed (sample1 : t... [ 0%] 0 of 3 [- ] process > make_uBAM [ 0%] 0 of 2 [d5/b500bc] process > Bwa (sample1 : tumor_DNA) [ 0%] 0 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [ 0%] 0 of 1 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > collectSampleInfo - [- ] process > multiQC - INFO: Mutect1 not available, skipping.... WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (23) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [ 0%] 0 of 3 [7a/e8c61d] process > make_uBAM (sample1 : normal... [ 0%] 0 of 2 [ce/540deb] process > Bwa (sample1 : normal_DNA) [ 0%] 0 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [ 0%] 0 of 1 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > collectSampleInfo - [- ] process > multiQC - WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... executor > slurm (23) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [ 0%] 0 of 3 [7a/e8c61d] process > make_uBAM (sample1 : normal... [ 0%] 0 of 2 [ce/540deb] process > Bwa (sample1 : normal_DNA) [ 0%] 0 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [ 0%] 0 of 1 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (25) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [ 0%] 0 of 1 [b3/2c4759] process > IntervalListToBed (BedFromI... [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [a5/92bbd5] process > FastQC_trimmed (sample1 : t... [ 33%] 1 of 3 [7a/e8c61d] process > make_uBAM (sample1 : normal... [ 0%] 0 of 2 [ce/540deb] process > Bwa (sample1 : normal_DNA) [ 0%] 0 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [ 0%] 0 of 1 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [ 0%] 0 of 3 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (26) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [ 0%] 0 of 1 [b3/2c4759] process > IntervalListToBed (BedFromI... [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [7a/e8c61d] process > make_uBAM (sample1 : normal... [ 0%] 0 of 2 [d5/b500bc] process > Bwa (sample1 : tumor_DNA) [ 50%] 1 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (26) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [ 0%] 0 of 1 [b3/2c4759] process > IntervalListToBed (BedFromI... [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [7a/e8c61d] process > make_uBAM (sample1 : normal... [ 50%] 1 of 2 [d5/b500bc] process > Bwa (sample1 : tumor_DNA) [ 50%] 1 of 2 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (26) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [- ] process > merge_uBAM_BAM [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (30) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [55/f29850] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (35) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [e2/f42555] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (41) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [a9/dc0e55] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (46) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [42/62e6b8] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (52) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [22/aaec49] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (58) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [a4/7d3a4d] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (64) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [cf/b85a52] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (68) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (68) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [ 0%] 0 of 1 [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (68) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [ 0%] 0 of 2 [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [8b/41f9aa] process > ScatteredIntervalListToBed ... [ 8%] 3 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [8d/ee81ee] process > ScatteredIntervalListToBed ... [ 18%] 7 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [d9/c7dd3f] process > ScatteredIntervalListToBed ... [ 30%] 12 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [a9/dc0e55] process > ScatteredIntervalListToBed ... [ 33%] 13 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [2a/c8f11f] process > ScatteredIntervalListToBed ... [ 50%] 20 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [05/6c652a] process > ScatteredIntervalListToBed ... [ 53%] 21 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [48/f7435c] process > ScatteredIntervalListToBed ... [ 73%] 29 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [75/2600e6] process > ScatteredIntervalListToBed ... [ 93%] 37 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [45/361fa8] process > ScatteredIntervalListToBed ... [ 95%] 38 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [45/361fa8] process > ScatteredIntervalListToBed ... [ 95%] 38 of 40 [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [ 0%] 0 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [ 0%] 0 of 1 [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - Error executing process > 'install_IEDB (Install IEDB)' Caused by: Process `install_IEDB (Install IEDB)` terminated with an error exit status (1) Command executed: CWD=`pwd` cd /opt/iedb/ wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz tar -xzvf IEDB_MHC_I-3.1.2.tar.gz cd mhc_i bash -c "./configure" cd /opt/iedb/ rm -f IEDB_MHC_I-3.1.2.tar.gz wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz tar -xzvf IEDB_MHC_II-3.1.6.tar.gz cd mhc_ii bash -c "python ./configure.py" cd /opt/iedb/ rm IEDB_MHC_II-3.1.6.tar.gz export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data mhcflurry-downloads fetch cd $CWD echo "OK" > .iedb_install_ok.chck Command exit status: 1 Command output: mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/make_P1_hist_frames.R mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/mhcfsa2psseq mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/NetMHCIIpan-4.0.pl mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netmhciipan_python_interface.py mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan.1 mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/requirements.txt mhc_ii/methods/netmhciipan-4.0-executable/MANIFEST.in mhc_ii/methods/netmhciipan-4.0-executable/setup.py mhc_ii/methods/netmhciipan-4.0-executable/example.py mhc_ii/methods/mhcii-comblib-percentile-data/ mhc_ii/methods/mhcii-comblib-percentile-data/README.rst mhc_ii/methods/mhcii-comblib-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-comblib-percentile-data/setup.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/create_percentile_data_file_pickle.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/__init__.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2018-11-26.p mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/requirements.txt mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2008-01-23.p mhc_ii/methods/mhcii-smmalign-percentile-data/ mhc_ii/methods/mhcii-smmalign-percentile-data/README.rst mhc_ii/methods/mhcii-smmalign-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-smmalign-percentile-data/setup.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/smmalign_percentile_distribution_2019-04-19.p mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/__init__.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.md mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/__init__.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/nn_align_percentile_distribution_2019-08-06.p mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/create_percentile_data_pickle_file_from_output_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.rst mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/setup.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/tests.py mhc_ii/length_rescaling.py mhc_ii/._mhc_II_binding.py mhc_ii/._README All prerequisites found! run MHCII tests... Command error: ./configure.py:33: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21160 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21318 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:13: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen('echo example').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21323 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21431 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:43: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21480 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback . ---------------------------------------------------------------------- Ran 9 tests in 8.833s OK Traceback (most recent call last): File "/opt/conda/bin/mhcflurry-downloads", line 8, in sys.exit(run()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 123, in run command_functions[args.subparser_name](args) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 194, in fetch_subcommand mkdir_p(get_downloads_dir()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 134, in mkdir_p os.makedirs(path) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/mhcflurry_data/2.0.0' Work dir: /data/kryan/neoant/nextNEOpi/work/e9/afd93c751c031d817fb02b8cae1a0f Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [100%] 40 of 40 ✔ [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [a8/ba91ae] process > MarkDuplicates (sample1 : n... [ 50%] 1 of 2 [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [100%] 1 of 1, failed: 1 ✘ [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'install_IEDB (Install IEDB)' Caused by: Process `install_IEDB (Install IEDB)` terminated with an error exit status (1) Command executed: CWD=`pwd` cd /opt/iedb/ wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz tar -xzvf IEDB_MHC_I-3.1.2.tar.gz cd mhc_i bash -c "./configure" cd /opt/iedb/ rm -f IEDB_MHC_I-3.1.2.tar.gz wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz tar -xzvf IEDB_MHC_II-3.1.6.tar.gz cd mhc_ii bash -c "python ./configure.py" cd /opt/iedb/ rm IEDB_MHC_II-3.1.6.tar.gz export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data mhcflurry-downloads fetch cd $CWD echo "OK" > .iedb_install_ok.chck Command exit status: 1 Command output: mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/make_P1_hist_frames.R mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/mhcfsa2psseq mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/NetMHCIIpan-4.0.pl mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netmhciipan_python_interface.py mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan.1 mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/requirements.txt mhc_ii/methods/netmhciipan-4.0-executable/MANIFEST.in mhc_ii/methods/netmhciipan-4.0-executable/setup.py mhc_ii/methods/netmhciipan-4.0-executable/example.py mhc_ii/methods/mhcii-comblib-percentile-data/ mhc_ii/methods/mhcii-comblib-percentile-data/README.rst mhc_ii/methods/mhcii-comblib-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-comblib-percentile-data/setup.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/create_percentile_data_file_pickle.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/__init__.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2018-11-26.p mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/requirements.txt mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2008-01-23.p mhc_ii/methods/mhcii-smmalign-percentile-data/ mhc_ii/methods/mhcii-smmalign-percentile-data/README.rst mhc_ii/methods/mhcii-smmalign-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-smmalign-percentile-data/setup.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/smmalign_percentile_distribution_2019-04-19.p mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/__init__.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.md mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/__init__.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/nn_align_percentile_distribution_2019-08-06.p mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/create_percentile_data_pickle_file_from_output_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.rst mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/setup.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/tests.py mhc_ii/length_rescaling.py mhc_ii/._mhc_II_binding.py mhc_ii/._README All prerequisites found! run MHCII tests... Command error: ./configure.py:33: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21160 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21318 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:13: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen('echo example').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21323 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21431 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:43: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21480 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback . ---------------------------------------------------------------------- Ran 9 tests in 8.833s OK Traceback (most recent call last): File "/opt/conda/bin/mhcflurry-downloads", line 8, in sys.exit(run()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 123, in run command_functions[args.subparser_name](args) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 194, in fetch_subcommand mkdir_p(get_downloads_dir()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 134, in mkdir_p os.makedirs(path) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/mhcflurry_data/2.0.0' Work dir: /data/kryan/neoant/nextNEOpi/work/e9/afd93c751c031d817fb02b8cae1a0f Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [100%] 40 of 40 ✔ [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [100%] 2 of 2 ✔ [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [100%] 1 of 1, failed: 1 ✘ [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - Error executing process > 'install_IEDB (Install IEDB)' Caused by: Process `install_IEDB (Install IEDB)` terminated with an error exit status (1) Command executed: CWD=`pwd` cd /opt/iedb/ wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz tar -xzvf IEDB_MHC_I-3.1.2.tar.gz cd mhc_i bash -c "./configure" cd /opt/iedb/ rm -f IEDB_MHC_I-3.1.2.tar.gz wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz tar -xzvf IEDB_MHC_II-3.1.6.tar.gz cd mhc_ii bash -c "python ./configure.py" cd /opt/iedb/ rm IEDB_MHC_II-3.1.6.tar.gz export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data mhcflurry-downloads fetch cd $CWD echo "OK" > .iedb_install_ok.chck Command exit status: 1 Command output: mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/make_P1_hist_frames.R mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/mhcfsa2psseq mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/NetMHCIIpan-4.0.pl mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netmhciipan_python_interface.py mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan.1 mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/requirements.txt mhc_ii/methods/netmhciipan-4.0-executable/MANIFEST.in mhc_ii/methods/netmhciipan-4.0-executable/setup.py mhc_ii/methods/netmhciipan-4.0-executable/example.py mhc_ii/methods/mhcii-comblib-percentile-data/ mhc_ii/methods/mhcii-comblib-percentile-data/README.rst mhc_ii/methods/mhcii-comblib-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-comblib-percentile-data/setup.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/create_percentile_data_file_pickle.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/__init__.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2018-11-26.p mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/requirements.txt mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2008-01-23.p mhc_ii/methods/mhcii-smmalign-percentile-data/ mhc_ii/methods/mhcii-smmalign-percentile-data/README.rst mhc_ii/methods/mhcii-smmalign-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-smmalign-percentile-data/setup.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/smmalign_percentile_distribution_2019-04-19.p mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/__init__.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.md mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/__init__.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/nn_align_percentile_distribution_2019-08-06.p mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/create_percentile_data_pickle_file_from_output_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.rst mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/setup.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/tests.py mhc_ii/length_rescaling.py mhc_ii/._mhc_II_binding.py mhc_ii/._README All prerequisites found! run MHCII tests... Command error: ./configure.py:33: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21160 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21318 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:13: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen('echo example').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21323 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21431 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:43: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21480 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback . ---------------------------------------------------------------------- Ran 9 tests in 8.833s OK Traceback (most recent call last): File "/opt/conda/bin/mhcflurry-downloads", line 8, in sys.exit(run()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 123, in run command_functions[args.subparser_name](args) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 194, in fetch_subcommand mkdir_p(get_downloads_dir()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 134, in mkdir_p os.makedirs(path) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/mhcflurry_data/2.0.0' Work dir: /data/kryan/neoant/nextNEOpi/work/e9/afd93c751c031d817fb02b8cae1a0f Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [100%] 40 of 40 ✔ [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [100%] 2 of 2 ✔ [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [100%] 1 of 1, failed: 1 ✘ [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - Error executing process > 'install_IEDB (Install IEDB)' Caused by: Process `install_IEDB (Install IEDB)` terminated with an error exit status (1) Command executed: CWD=`pwd` cd /opt/iedb/ wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz tar -xzvf IEDB_MHC_I-3.1.2.tar.gz cd mhc_i bash -c "./configure" cd /opt/iedb/ rm -f IEDB_MHC_I-3.1.2.tar.gz wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz tar -xzvf IEDB_MHC_II-3.1.6.tar.gz cd mhc_ii bash -c "python ./configure.py" cd /opt/iedb/ rm IEDB_MHC_II-3.1.6.tar.gz export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data mhcflurry-downloads fetch cd $CWD echo "OK" > .iedb_install_ok.chck Command exit status: 1 Command output: mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/make_P1_hist_frames.R mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/mhcfsa2psseq mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/NetMHCIIpan-4.0.pl mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netmhciipan_python_interface.py mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan.1 mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/requirements.txt mhc_ii/methods/netmhciipan-4.0-executable/MANIFEST.in mhc_ii/methods/netmhciipan-4.0-executable/setup.py mhc_ii/methods/netmhciipan-4.0-executable/example.py mhc_ii/methods/mhcii-comblib-percentile-data/ mhc_ii/methods/mhcii-comblib-percentile-data/README.rst mhc_ii/methods/mhcii-comblib-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-comblib-percentile-data/setup.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/create_percentile_data_file_pickle.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/__init__.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2018-11-26.p mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/requirements.txt mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2008-01-23.p mhc_ii/methods/mhcii-smmalign-percentile-data/ mhc_ii/methods/mhcii-smmalign-percentile-data/README.rst mhc_ii/methods/mhcii-smmalign-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-smmalign-percentile-data/setup.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/smmalign_percentile_distribution_2019-04-19.p mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/__init__.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.md mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/__init__.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/nn_align_percentile_distribution_2019-08-06.p mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/create_percentile_data_pickle_file_from_output_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.rst mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/setup.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/tests.py mhc_ii/length_rescaling.py mhc_ii/._mhc_II_binding.py mhc_ii/._README All prerequisites found! run MHCII tests... Command error: ./configure.py:33: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21160 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21318 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:13: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen('echo example').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21323 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21431 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:43: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21480 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback . ---------------------------------------------------------------------- Ran 9 tests in 8.833s OK Traceback (most recent call last): File "/opt/conda/bin/mhcflurry-downloads", line 8, in sys.exit(run()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 123, in run command_functions[args.subparser_name](args) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 194, in fetch_subcommand mkdir_p(get_downloads_dir()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 134, in mkdir_p os.makedirs(path) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/mhcflurry_data/2.0.0' Work dir: /data/kryan/neoant/nextNEOpi/work/e9/afd93c751c031d817fb02b8cae1a0f Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Failed to invoke `workflow.onComplete` event handler -- Check script 'nextNEOpi.nf' at line: 6742 or see '.nextflow.log' file for more details executor > slurm (70) [- ] process > merge_fastq - [57/4bbcde] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [15/8489af] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [29/50ca8f] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [ce/8142ce] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [b3/2c4759] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [b0/e7cd12] process > ScatteredIntervalListToBed ... [100%] 40 of 40 ✔ [4d/72d214] process > FastQC (sample1 : tumor_DNA) [100%] 3 of 3 ✔ [3a/8a5824] process > fastp (sample1 : normal_DNA) [100%] 3 of 3 ✔ [51/94bfcd] process > FastQC_trimmed (sample1 : n... [100%] 3 of 3 ✔ [d5/9378e6] process > make_uBAM (sample1 : tumor_... [100%] 2 of 2 ✔ [ce/540deb] process > Bwa (sample1 : normal_DNA) [100%] 2 of 2 ✔ [8c/e263c1] process > merge_uBAM_BAM (sample1 : t... [100%] 2 of 2 ✔ [54/ce38dd] process > MarkDuplicates (sample1 : t... [100%] 2 of 2 ✔ [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [32/f06384] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [ac/56b775] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [90/3f3ba0] process > pre_map_hla_RNA (sample1) [100%] 1 of 1 ✔ [ef/63f439] process > OptiType_RNA (sample1) [100%] 1 of 1 ✔ [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [e9/afd93c] process > install_IEDB (Install IEDB) [100%] 1 of 1, failed: 1 ✘ [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > immunogenicity_scoring - [b8/2bfa06] process > mixcr (sample1 : normal_DNA) [100%] 3 of 3 ✔ [- ] process > collectSampleInfo - [- ] process > multiQC - WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Error executing process > 'install_IEDB (Install IEDB)' Caused by: Process `install_IEDB (Install IEDB)` terminated with an error exit status (1) Command executed: CWD=`pwd` cd /opt/iedb/ wget https://downloads.iedb.org/tools/mhci/3.1.2/IEDB_MHC_I-3.1.2.tar.gz tar -xzvf IEDB_MHC_I-3.1.2.tar.gz cd mhc_i bash -c "./configure" cd /opt/iedb/ rm -f IEDB_MHC_I-3.1.2.tar.gz wget https://downloads.iedb.org/tools/mhcii/3.1.6/IEDB_MHC_II-3.1.6.tar.gz tar -xzvf IEDB_MHC_II-3.1.6.tar.gz cd mhc_ii bash -c "python ./configure.py" cd /opt/iedb/ rm IEDB_MHC_II-3.1.6.tar.gz export MHCFLURRY_DATA_DIR=/opt/mhcflurry_data mhcflurry-downloads fetch cd $CWD echo "OK" > .iedb_install_ok.chck Command exit status: 1 Command output: mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/make_P1_hist_frames.R mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/Linux_x86_64/bin/mhcfsa2psseq mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/NetMHCIIpan-4.0.pl mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netmhciipan_python_interface.py mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/netMHCIIpan.1 mhc_ii/methods/netmhciipan-4.0-executable/netmhciipan_4_0_executable/requirements.txt mhc_ii/methods/netmhciipan-4.0-executable/MANIFEST.in mhc_ii/methods/netmhciipan-4.0-executable/setup.py mhc_ii/methods/netmhciipan-4.0-executable/example.py mhc_ii/methods/mhcii-comblib-percentile-data/ mhc_ii/methods/mhcii-comblib-percentile-data/README.rst mhc_ii/methods/mhcii-comblib-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-comblib-percentile-data/setup.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/ mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/create_percentile_data_file_pickle.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/__init__.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2018-11-26.p mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/requirements.txt mhc_ii/methods/mhcii-comblib-percentile-data/mhcii_comblib_percentile_data/comblib_percentile_distribution_2008-01-23.p mhc_ii/methods/mhcii-smmalign-percentile-data/ mhc_ii/methods/mhcii-smmalign-percentile-data/README.rst mhc_ii/methods/mhcii-smmalign-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-smmalign-percentile-data/setup.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/ mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/smmalign_percentile_distribution_2019-04-19.p mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/__init__.py mhc_ii/methods/mhcii-smmalign-percentile-data/mhcii_smmalign_percentile_data/make_pickle_from_data_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.md mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/ mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/tests/PercentileManager_Tests.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/__init__.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/nn_align_percentile_distribution_2019-08-06.p mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/mhcii_netmhcii_2_3_percentile_data/create_percentile_data_pickle_file_from_output_files.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/README.rst mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/MANIFEST.in mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/setup.py mhc_ii/methods/mhcii-netmhcii-2.3-percentile-data/tests.py mhc_ii/length_rescaling.py mhc_ii/._mhc_II_binding.py mhc_ii/._README All prerequisites found! run MHCII tests... Command error: ./configure.py:33: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21160 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21318 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:13: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen('echo example').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21323 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21431 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:43: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ./opt/conda/lib/python3.8/subprocess.py:942: ResourceWarning: subprocess 21480 is still running _warn("subprocess %s is still running" % self.pid, ResourceWarning: Enable tracemalloc to get the object allocation traceback ./configure.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='UTF-8'> result=os.popen(cmd).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback . ---------------------------------------------------------------------- Ran 9 tests in 8.833s OK Traceback (most recent call last): File "/opt/conda/bin/mhcflurry-downloads", line 8, in sys.exit(run()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 123, in run command_functions[args.subparser_name](args) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 194, in fetch_subcommand mkdir_p(get_downloads_dir()) File "/opt/conda/lib/python3.8/site-packages/mhcflurry/downloads_command.py", line 134, in mkdir_p os.makedirs(path) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/mhcflurry_data/2.0.0' Work dir: /data/kryan/neoant/nextNEOpi/work/e9/afd93c751c031d817fb02b8cae1a0f Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Failed to invoke `workflow.onComplete` event handler -- Check script 'nextNEOpi.nf' at line: 6742 or see '.nextflow.log' file for more details Elapsed time: 0 days 00 hr 06 min 37 sec