N E X T F L O W ~ version 20.10.0 Launching `nextNEOpi.nf` [gloomy_tuckerman] - revision: 3eb7892941 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 -bg run nextNEOpi.nf --batchFile batchFile.csv -config conf/params.config --outputDir nextNeoPi_results --trim_adapters false --trim_adapters_RNAseq false --use_NetChop false --accept_license -N k.ryan45@nuigalway.ie -profile singularity Working Directory: /home/kevin/sw/nextNEOpi Output Directory: nextNeoPi_results I N P U T batch file: batchFile.csv Please check --help for further instruction ------------------------------------------------------------------------- WARN: I have read and accept the licence terms tmpDir: /tmp/kevin/nextNEOpi Pipeline Name : icbi/nextNEOpi Pipeline Version : 1.0 Batch file : batchFile.csv Read length : 150 Exome capture kit : sureSelectV6 Fasta Ref : /home/kevin/sw/nextNEOpi/resources/references/hg38/gdc/GRCh38.d1.vd1/fasta/GRCh38.d1.vd1.fa MillsGold : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf hcSNPS1000G : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz HapMap : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/hapmap_3.3.hg38.vcf.gz Cosmic : /home/kevin/sw/nextNEOpi/resources/databases/cosmic/CosmicCodingMuts.vcf DBSNP : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.dbsnp138.vcf GnomAD : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/GetPileupSummaries/small_exac_common_3.hg38.vcf GnomADfull : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/gnomAD/af-only-gnomad.hg38.vcf.gz KnownIndels : /home/kevin/sw/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.known_indels.vcf BlastDB : /home/kevin/sw/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 : /home/kevin/sw/nextNEOpi/work TMP dir : /tmp/kevin/nextNEOpi Current home : /home/kevin Current user : kevin Current path : /home/kevin/sw/nextNEOpi JAVA_Xmx : -Xmx64G Picard maxRecordsInRam : 4194304 Script dir : /home/kevin/sw/nextNEOpi Config Profile : singularity ------------------------------------------------------------------------- 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 /home/kevin/sw/hlahd.1.4.0/bin/hlahd.sh at: /home/kevin/sw/hlahd.1.4.0/bin/hlahd.sh Found /home/kevin/sw/java-se-7u75-ri/bin/java at: /home/kevin/sw/java-se-7u75-ri/bin/java Found /home/kevin/sw/mutect1/muTect-1.1.4.jar at: /home/kevin/sw/mutect1/muTect-1.1.4.jar [e5/d874fe] Submitted process > FastQC (sample1 : tumor_RNA) [76/d9494b] Submitted process > BaitsBedToIntervalList (BaitsBedToIntervalList) [1a/050cdf] Submitted process > FastQC (sample1 : normal_DNA) [0d/291a21] Submitted process > RegionsBedToIntervalList (RegionsBedToIntervalList) [58/3a0092] Submitted process > FastQC (sample1 : tumor_DNA) [d0/5f7daf] Submitted process > make_uBAM (sample1 : normal_DNA) [e1/8f07a9] Submitted process > make_uBAM (sample1 : tumor_DNA) [d7/59c10e] Submitted process > install_conda_GATK3 (install GATK3) WARN: WARNING: IEDB yet not installed, starting installation. This may take a while... [a8/8865a2] Submitted process > make_CNVkit_access_file (mkCNVkitaccess) [98/a03d85] Submitted process > install_IEDB (Install IEDB) [cf/b66f62] Submitted process > install_mixMHC2pred (install mixMHC2pred) [0b/0cc6e3] Submitted process > install_IGS (install IGS) [2b/1d3f7a] Submitted process > preprocessIntervalList (preprocessIntervalList) [83/e6254b] Submitted process > Bwa (sample1 : tumor_DNA) [68/c4f407] Submitted process > Bwa (sample1 : normal_DNA) [38/080f5d] Submitted process > pre_map_hla_RNA (sample1) [c7/7fae32] Submitted process > mixcr (sample1 : normal_DNA) [7c/f6d12c] Submitted process > mixcr (sample1 : tumor_DNA) [02/c225a0] Submitted process > SplitIntervals (SplitIntervals) [36/041457] Submitted process > mixcr (sample1 : tumor_RNA) [dd/d54679] Submitted process > IntervalListToBed (BedFromIntervalList) [09/57dc5b] Submitted process > merge_uBAM_BAM (sample1 : tumor_DNA) [ed/3eaf19] Submitted process > merge_uBAM_BAM (sample1 : normal_DNA) [18/ef0b3d] Submitted process > OptiType_RNA (sample1) [c6/02dd28] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [42/711ada] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [ec/fa006f] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [e7/977b67] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [e7/fc2392] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [1f/8dae8c] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [fb/8f6359] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [3d/e1511a] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [01/c2b79e] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [fe/56c0f3] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [53/05a202] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [41/6d737e] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [98/de748e] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [58/59d078] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [ae/1db1d7] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [0e/e56ab3] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [c8/909516] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [dd/dbd7c1] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [23/fafde3] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [56/aba0dd] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [78/eefc3e] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [fe/a95f24] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [1b/539cae] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [87/6cd0f2] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [4a/cb7237] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [d0/44e40d] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [f8/1b93eb] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [1f/713429] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [79/40af22] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [6b/5ebe29] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [97/a4037d] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [f6/1bf678] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [02/bb57f2] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [6d/866885] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [64/3325ee] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [23/52e1ec] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [5b/fa1736] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [54/e070be] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [75/65ea02] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [98/55ae85] Submitted process > ScatteredIntervalListToBed (ScatteredIntervalListToBed) [54/621535] Submitted process > MarkDuplicates (sample1 : tumor_DNA) [fd/f23fa9] Submitted process > MarkDuplicates (sample1 : normal_DNA) [0a/b057b2] Submitted process > alignmentMetrics (sample1 : tumor_DNA) [6b/014306] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [e1/e6a4eb] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [52/f21ff0] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [32/769e23] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [fa/b8df34] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [60/61a11c] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [89/665594] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [58/e45658] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [fc/f5e444] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [7d/4b72f9] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [1e/311d4d] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [6e/d33b2d] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [de/78a236] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [79/876d3a] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [4d/7cc286] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [70/a6fb90] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [f9/d8c869] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [c5/e98ab7] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [c1/6864be] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [70/59b3f4] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [f8/7617d6] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [a4/5db4fd] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) [f3/f69a8e] Submitted process > scatterBaseRecalGATK4 (sample1 : tumor_DNA) 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/3.1.5/IEDB_MHC_II-3.1.5.tar.gz tar -xzvf IEDB_MHC_II-3.1.5.tar.gz cd mhc_ii ./configure.py cd /opt/iedb/ rm IEDB_MHC_II-3.1.5.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/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! environemnt variable TMPDIR is not set. /tmp will be used for temporary files run MHCII tests... Command error: 2022-05-06 17:02:30 (17.1 MB/s) - ‘IEDB_MHC_II-3.1.5.tar.gz’ saved [780066105/780066105] .list index out of range F.FF.list index out of range Flist index out of range F. ====================================================================== FAIL: test_consensus (__main__.Test_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "./configure.py", line 19, in test_consensus self.assertEqual(result, 'allele\tseq_num\tstart\tend\tlength\tpeptide\tconsensus_percentile_rank\tadjusted_consensus_percentile_rank\tcomblib_core\tcomblib_score\tcomblib_rank\tadjusted_comblib_rank\tsmm_align_core\tsmm_align_ic50\tsmm_align_rank\tadjusted_smm_align_rank\tnn_align_core\tnn_align_ic50\tnn_align_rank\tadjusted_nn_align_rank\tsturniolo_core\tsturniolo_score\tsturniolo_rank\tadjusted_sturniolo_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tEGVSGATWVDLVLEG\t59.0\t59.00\t-\t-\t-\t-\tVSGATWVDL\t5932.0\t59.0\t59.00\tTWVDLVLEG\t3356.9\t50.0\t50.00\tVSGATWVDL\t-1.34\t88.0\t88.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tRDFLEGVSGATWVDL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t8523.0\t69.0\t69.00\tVSGATWVDL\t12707.7\t85.0\t85.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tDFLEGVSGATWVDLV\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18841.0\t85.0\t85.00\tVSGATWVDL\t10634.4\t81.0\t81.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tFLEGVSGATWVDLVL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18363.0\t85.0\t85.00\tVSGATWVDL\t8154.8\t74.0\t74.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tMSNRDFLEGVSGATW\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9343.0\t71.0\t71.00\tDFLEGVSGA\t17372.9\t92.0\t92.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tSNRDFLEGVSGATWV\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t8986.0\t70.0\t70.00\tDFLEGVSGA\t18531.9\t93.0\t93.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tNRDFLEGVSGATWVD\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9085.0\t70.0\t70.00\tDFLEGVSGA\t18458.2\t93.0\t93.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tLEGVSGATWVDLVLE\t88.0\t88.00\t-\t-\t-\t-\tSGATWVDLV\t26621.0\t91.0\t91.00\tVSGATWVDL\t5473.3\t63.0\t63.00\tVSGATWVDL\t-1.34\t88.0\t88.00\n') AssertionError: '' != 'allele\tseq_num\tstart\tend\tlength\tpeptide\tconsensus_percentile_rank\tadjusted_consensus_percentile_rank\tcomblib_core\tcomblib_score\tcomblib_rank\tadjusted_comblib_rank\tsmm_align_core\tsmm_align_ic50\tsmm_align_rank\tadjusted_smm_align_rank\tnn_align_core\tnn_align_ic50\tnn_align_rank\tadjusted_nn_align_rank\tsturniolo_core\tsturniolo_score\tsturniolo_rank\tadjusted_sturniolo_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tEGVSGATWVDLVLEG\t59.0\t59.00\t-\t-\t-\t-\tVSGATWVDL\t5932.0\t59.0\t59.00\tTWVDLVLEG\t3356.9\t50.0\t50.00\tVSGATWVDL\t-1.34\t88.0\t88.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tRDFLEGVSGATWVDL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t8523.0\t69.0\t69.00\tVSGATWVDL\t12707.7\t85.0\t85.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tDFLEGVSGATWVDLV\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18841.0\t85.0\t85.00\tVSGATWVDL\t10634.4\t81.0\t81.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tFLEGVSGATWVDLVL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18363.0\t85.0\t85.00\tVSGATWVDL\t8154.8\t74.0\t74.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tMSNRDFLEGVSGATW\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9343.0\t71.0\t71.00\tDFLEGVSGA\t17372.9\t92.0\t92.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tSNRDFLEGVSGATWV\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t8986.0\t70.0\t70.00\tDFLEGVSGA\t18531.9\t93.0\t93.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tNRDFLEGVSGATWVD\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9085.0\t70.0\t70.00\tDFLEGVSGA\t18458.2\t93.0\t93.00\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tLEGVSGATWVDLVLE\t88.0\t88.00\t-\t-\t-\t-\tSGATWVDLV\t26621.0\t91.0\t91.00\tVSGATWVDL\t5473.3\t63.0\t63.00\tVSGATWVDL\t-1.34\t88.0\t88.00\n' ====================================================================== FAIL: test_netmhciipan (__main__.Test_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "./configure.py", line 34, in test_netmhciipan self.assertEqual(result, 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tTWVDLVLEG\tEGVSGATWVDLVLEG\t6159.57\t71.0\t71.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tGATWVDLVL\tFLEGVSGATWVDLVL\t9173.76\t84.0\t84.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tGATWVDLVL\tLEGVSGATWVDLVLE\t9199.80\t84.0\t84.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tSNRDFLEGV\tMSNRDFLEGVSGATW\t9532.78\t85.0\t85.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tLEGVSGATW\tRDFLEGVSGATWVDL\t10018.37\t86.0\t86.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tLEGVSGATW\tDFLEGVSGATWVDLV\t10379.28\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tLEGVSGATW\tSNRDFLEGVSGATWV\t10436.49\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tLEGVSGATW\tNRDFLEGVSGATWVD\t11966.01\t91.0\t91.00\n' ) AssertionError: 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\n' != 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tTWVDLVLEG\tEGVSGATWVDLVLEG\t6159.57\t71.0\t71.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tGATWVDLVL\tFLEGVSGATWVDLVL\t9173.76\t84.0\t84.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tGATWVDLVL\tLEGVSGATWVDLVLE\t9199.80\t84.0\t84.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tSNRDFLEGV\tMSNRDFLEGVSGATW\t9532.78\t85.0\t85.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tLEGVSGATW\tRDFLEGVSGATWVDL\t10018.37\t86.0\t86.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tLEGVSGATW\tDFLEGVSGATWVDLV\t10379.28\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tLEGVSGATW\tSNRDFLEGVSGATWV\t10436.49\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tLEGVSGATW\tNRDFLEGVSGATWVD\t11966.01\t91.0\t91.00\n' ====================================================================== FAIL: test_nn (__main__.Test_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "./configure.py", line 39, in test_nn self.assertEqual(result, 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tTWVDLVLEG\tEGVSGATWVDLVLEG\t3356.90\t50.0\t50.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tVSGATWVDL\tLEGVSGATWVDLVLE\t5473.30\t63.0\t63.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tVSGATWVDL\tFLEGVSGATWVDLVL\t8154.80\t74.0\t74.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tVSGATWVDL\tDFLEGVSGATWVDLV\t10634.40\t81.0\t81.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tVSGATWVDL\tRDFLEGVSGATWVDL\t12707.70\t85.0\t85.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tDFLEGVSGA\tMSNRDFLEGVSGATW\t17372.90\t92.0\t92.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tDFLEGVSGA\tNRDFLEGVSGATWVD\t18458.20\t93.0\t93.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tDFLEGVSGA\tSNRDFLEGVSGATWV\t18531.90\t93.0\t93.00\n') AssertionError: 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\n' != 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tTWVDLVLEG\tEGVSGATWVDLVLEG\t3356.90\t50.0\t50.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tVSGATWVDL\tLEGVSGATWVDLVLE\t5473.30\t63.0\t63.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tVSGATWVDL\tFLEGVSGATWVDLVL\t8154.80\t74.0\t74.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tVSGATWVDL\tDFLEGVSGATWVDLV\t10634.40\t81.0\t81.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tVSGATWVDL\tRDFLEGVSGATWVDL\t12707.70\t85.0\t85.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tDFLEGVSGA\tMSNRDFLEGVSGATW\t17372.90\t92.0\t92.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tDFLEGVSGA\tNRDFLEGVSGATWVD\t18458.20\t93.0\t93.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tDFLEGVSGA\tSNRDFLEGVSGATWV\t18531.90\t93.0\t93.00\n' ====================================================================== FAIL: test_recommended (__main__.Test_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "./configure.py", line 24, in test_recommended self.assertEqual(result, 'allele\tseq_num\tstart\tend\tlength\tmethod\tpeptide\tconsensus_percentile_rank\tadjusted_consensus_percentile_rank\tcomblib_core\tcomblib_score\tcomblib_rank\tadjusted_comblib_rank\tsmm_align_core\tsmm_align_ic50\tsmm_align_rank\tadjusted_smm_align_rank\tnn_align_core\tnn_align_ic50\tnn_align_rank\tadjusted_nn_align_rank\tnetmhciipan_core\tnetmhciipan_ic50\tnetmhciipan_rank\tadjusted_netmhciipan_rank\tsturniolo_core\tsturniolo_score\tsturniolo_rank\tadjusted_sturniolo_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tSMM-NN-Sturniolo\tEGVSGATWVDLVLEG\t59.0\t59.00\t-\t-\t-\t-\tVSGATWVDL\t5932.0\t59.0\t59.00\tTWVDLVLEG\t3356.9\t50.0\t50.00\t-\t-\t-\t-\tVSGATWVDL\t-1.34\t88.0\t88.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tSMM-NN-Sturniolo\tRDFLEGVSGATWVDL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t8523.0\t69.0\t69.00\tVSGATWVDL\t12707.7\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tSMM-NN-Sturniolo\tDFLEGVSGATWVDLV\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18841.0\t85.0\t85.00\tVSGATWVDL\t10634.4\t81.0\t81.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tSMM-NN-Sturniolo\tFLEGVSGATWVDLVL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18363.0\t85.0\t85.00\tVSGATWVDL\t8154.8\t74.0\t74.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tSMM-NN-Sturniolo\tMSNRDFLEGVSGATW\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9343.0\t71.0\t71.00\tDFLEGVSGA\t17372.9\t92.0\t92.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tSMM-NN-Sturniolo\tSNRDFLEGVSGATWV\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t8986.0\t70.0\t70.00\tDFLEGVSGA\t18531.9\t93.0\t93.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tSMM-NN-Sturniolo\tNRDFLEGVSGATWVD\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9085.0\t70.0\t70.00\tDFLEGVSGA\t18458.2\t93.0\t93.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tSMM-NN-Sturniolo\tLEGVSGATWVDLVLE\t88.0\t88.00\t-\t-\t-\t-\tSGATWVDLV\t26621.0\t91.0\t91.00\tVSGATWVDL\t5473.3\t63.0\t63.00\t-\t-\t-\t-\tVSGATWVDL\t-1.34\t88.0\t88.00\n') AssertionError: '' != 'allele\tseq_num\tstart\tend\tlength\tmethod\tpeptide\tconsensus_percentile_rank\tadjusted_consensus_percentile_rank\tcomblib_core\tcomblib_score\tcomblib_rank\tadjusted_comblib_rank\tsmm_align_core\tsmm_align_ic50\tsmm_align_rank\tadjusted_smm_align_rank\tnn_align_core\tnn_align_ic50\tnn_align_rank\tadjusted_nn_align_rank\tnetmhciipan_core\tnetmhciipan_ic50\tnetmhciipan_rank\tadjusted_netmhciipan_rank\tsturniolo_core\tsturniolo_score\tsturniolo_rank\tadjusted_sturniolo_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tSMM-NN-Sturniolo\tEGVSGATWVDLVLEG\t59.0\t59.00\t-\t-\t-\t-\tVSGATWVDL\t5932.0\t59.0\t59.00\tTWVDLVLEG\t3356.9\t50.0\t50.00\t-\t-\t-\t-\tVSGATWVDL\t-1.34\t88.0\t88.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tSMM-NN-Sturniolo\tRDFLEGVSGATWVDL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t8523.0\t69.0\t69.00\tVSGATWVDL\t12707.7\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tSMM-NN-Sturniolo\tDFLEGVSGATWVDLV\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18841.0\t85.0\t85.00\tVSGATWVDL\t10634.4\t81.0\t81.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tSMM-NN-Sturniolo\tFLEGVSGATWVDLVL\t85.0\t85.00\t-\t-\t-\t-\tFLEGVSGAT\t18363.0\t85.0\t85.00\tVSGATWVDL\t8154.8\t74.0\t74.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tSMM-NN-Sturniolo\tMSNRDFLEGVSGATW\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9343.0\t71.0\t71.00\tDFLEGVSGA\t17372.9\t92.0\t92.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tSMM-NN-Sturniolo\tSNRDFLEGVSGATWV\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t8986.0\t70.0\t70.00\tDFLEGVSGA\t18531.9\t93.0\t93.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tSMM-NN-Sturniolo\tNRDFLEGVSGATWVD\t87.0\t87.00\t-\t-\t-\t-\tFLEGVSGAT\t9085.0\t70.0\t70.00\tDFLEGVSGA\t18458.2\t93.0\t93.00\t-\t-\t-\t-\tFLEGVSGAT\t-1.2\t87.0\t87.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tSMM-NN-Sturniolo\tLEGVSGATWVDLVLE\t88.0\t88.00\t-\t-\t-\t-\tSGATWVDLV\t26621.0\t91.0\t91.00\tVSGATWVDL\t5473.3\t63.0\t63.00\t-\t-\t-\t-\tVSGATWVDL\t-1.34\t88.0\t88.00\n' ====================================================================== FAIL: test_smm (__main__.Test_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "./configure.py", line 44, in test_smm self.assertEqual(result, 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tVSGATWVDL\tEGVSGATWVDLVLEG\t5932.00\t59.0\t59.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tFLEGVSGAT\tRDFLEGVSGATWVDL\t8523.00\t69.0\t69.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tFLEGVSGAT\tSNRDFLEGVSGATWV\t8986.00\t70.0\t70.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tFLEGVSGAT\tNRDFLEGVSGATWVD\t9085.00\t70.0\t70.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tFLEGVSGAT\tMSNRDFLEGVSGATW\t9343.00\t71.0\t71.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tFLEGVSGAT\tFLEGVSGATWVDLVL\t18363.00\t85.0\t85.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tFLEGVSGAT\tDFLEGVSGATWVDLV\t18841.00\t85.0\t85.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tSGATWVDLV\tLEGVSGATWVDLVLE\t26621.00\t91.0\t91.00\n') AssertionError: '' != 'allele\tseq_num\tstart\tend\tlength\tcore_peptide\tpeptide\tic50\tpercentile_rank\tadjusted_rank\nHLA-DRB1*03:01\t1\t8\t22\t15\tVSGATWVDL\tEGVSGATWVDLVLEG\t5932.00\t59.0\t59.00\nHLA-DRB1*03:01\t1\t4\t18\t15\tFLEGVSGAT\tRDFLEGVSGATWVDL\t8523.00\t69.0\t69.00\nHLA-DRB1*03:01\t1\t2\t16\t15\tFLEGVSGAT\tSNRDFLEGVSGATWV\t8986.00\t70.0\t70.00\nHLA-DRB1*03:01\t1\t3\t17\t15\tFLEGVSGAT\tNRDFLEGVSGATWVD\t9085.00\t70.0\t70.00\nHLA-DRB1*03:01\t1\t1\t15\t15\tFLEGVSGAT\tMSNRDFLEGVSGATW\t9343.00\t71.0\t71.00\nHLA-DRB1*03:01\t1\t6\t20\t15\tFLEGVSGAT\tFLEGVSGATWVDLVL\t18363.00\t85.0\t85.00\nHLA-DRB1*03:01\t1\t5\t19\t15\tFLEGVSGAT\tDFLEGVSGATWVDLV\t18841.00\t85.0\t85.00\nHLA-DRB1*03:01\t1\t7\t21\t15\tSGATWVDLV\tLEGVSGATWVDLVLE\t26621.00\t91.0\t91.00\n' ---------------------------------------------------------------------- Ran 9 tests in 5.324s FAILED (failures=5) Work dir: /home/kevin/sw/nextNEOpi/work/98/a03d85701770d614fd985dc27566c5 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Execution cancelled -- Finishing pending tasks before exit