Long error using the code below

[HyojeenLee]

#I am now analysing the single cell RNA seq data for the somatic mutation calling.
#1. I made BAM and BAM.BAI file with minimap2 using the command below

(minimap for fastq to SAM)

./minimap2 -a hg38.mmi xx_HL.fastq > alignment.sam

(samtools 'view' for SAM to BAM)
./samtools view -S -b ../minimap2/ESCC_align_minimap2_index_HL/20221120_minimap2_${file}HL.sam> ESCC_BAM_HL/20221123_BAM${file}_HL.bam

(samtools for BAM to sorted to BAI)
./samtools sort ESCC_BAM_HL/20221123_BAM_${file}HL.bam -o ESCC_sorted_BAM_HL/20221201_sorted_BAM${file}_HL.sorted.bam

./samtools index ESCC_sorted_BAM_HL/20221201_sorted_BAM_${file}HL.sorted.bam ESCC_sorted_BAM_BAI_HL/20221201_ESCC_sortedBAMBAI${file}_HL.bam.bai

#2. and used Strelka command like below (format of RESA's suggested input prerequisite for variant calling):

conda activate strelka; python strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py --bam 21_N4_split/AGNCGCTT.bam --referenceFasta hg38.fa --rna --runDir ./strelka_split_out/ESCC_21_N4_NUC_split_test; ./strelka_split_out/ESCC_21_N4_NUC_split_test/runWorkflow.py -m local -j 4

#Then, I got an long error like below:

[2022-12-02T04:50:53.559908Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenome
Segment_chromId_000_chr1_0019' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-
2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size
49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/ge
nomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing
--stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId
_000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch6
0/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/j
c2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4
_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/conf
ig/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:50:53.569852Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Er
ror Message:
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] La
st 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.476438Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scrat
ch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.477711Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.481713Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' whi
le attempting to read BAM/CRAM file:
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.483178Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/A
GNCGCTT.bam'
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.484195Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_selected_region: chr1:225245890-237101754
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.485154Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] no bam record currently set
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.486134Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019]
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.487068Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x
86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping
-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpd
ir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /g
pfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.x
ml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/
km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka
/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.
bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorMod
el.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.488035Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] version: 2.9.10
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.488978Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.489907Z] [c23n05.ruddle.hpc.yale.i
nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] compiler: g++-6.3.1
[2022-12-02T04:50:53.618353Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining ta
sks to complete.
[2022-12-02T04:50:54.358430Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenome
Segment_chromId_000_chr1_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-
2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49
--min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/geno
meSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing -
-stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_0
00_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/
lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2
545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_s
plit/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:50:54.362504Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Error Message:
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.256168Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.257477Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.266638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.267753Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.268751Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_selected_region: chr1:11854670-23710535
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.269712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] no bam record currently set
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.270701Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001]
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.271758Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.272849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] version: 2.9.10
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.273810Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.274712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] compiler: g++-6.3.1
[2022-12-02T04:50:54.403870Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_001_chr10_0010' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:50:54.407493Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Error Message:
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.323526Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.327089Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.332459Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334074Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334740Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_selected_region: chr10:111497454-122648036
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.336271Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] no bam record currently set
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.341764Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010]
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.342722Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.345071Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] version: 2.9.10
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.346361Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.348638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] compiler: g++-6.3.1
[2022-12-02T04:50:54.414580Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:50:54.418518Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Error Message:
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.310092Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.320856Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.326367Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.327457Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.328218Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_selected_region: chr1:35564806-47420671
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.329242Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] no bam record currently set
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.330175Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003]
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.331350Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.332391Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] version: 2.9.10
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.333437Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334637Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] compiler: g++-6.3.1
[2022-12-02T04:51:00.339176Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2022-12-02T04:51:10.059849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2022-12-02T04:51:10.063988Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGen
omeSegment_chromId_000_chr1_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strel
ka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size
49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/g
enomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasin
g --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromI
d_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch
60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/
jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N
4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/con
fig/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:51:10.067254Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003]
Error Message:
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003]
Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.310092Z] [c23n05.ruddle.hpc.yal
e.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/sc
ratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.320856Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.326367Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.327457Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.328218Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_selected_region: chr1:35564806-47420671
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.329242Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] no bam record currently set
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.330175Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003]
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.331350Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.332391Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] version: 2.9.10
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.333437Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334637Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] compiler: g++-6.3.1
[2022-12-02T04:51:10.074609Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_001_chr10_0010' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:51:10.077994Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Error Message:
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.323526Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.327089Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.332459Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334074Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334740Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_selected_region: chr10:111497454-122648036
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.336271Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] no bam record currently set
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.341764Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010]
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.342722Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.345071Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] version: 2.9.10
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.346361Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.348638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] compiler: g++-6.3.1
[2022-12-02T04:51:10.084854Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow'
[2022-12-02T04:51:10.087670Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0019' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:51:10.091207Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Error Message:
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.476438Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.477711Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.481713Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.483178Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.484195Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_selected_region: chr1:225245890-237101754
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.485154Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] no bam record currently set
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.486134Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019]
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.487068Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.488035Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] version: 2.9.10
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.488978Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.489907Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] compiler: g++-6.3.1
[2022-12-02T04:51:10.097679Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json'
[2022-12-02T04:51:10.100576Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Error Message:
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Last 11 stderr lines from task (of 11 total lines):
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.256168Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.257477Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.266638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.267753Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam'
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.268751Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_selected_region: chr1:11854670-23710535
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.269712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] no bam record currently set
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.270701Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001]
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.271758Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.272849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] version: 2.9.10
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.273810Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] buildTime: 2018-11-08T00:32:40.775496Z
[2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.274712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] compiler: g++-6.3.1

#What should I change?Thank you