/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector:60: SyntaxWarning: invalid escape sequence '\|'
"""
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/fusion_pair_to_mini_genome_join.pl --fusions 046i_bl9_PDAC_AllprepFFPE.fusionreport.tsv --gtf /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE --shrink_introns --max_intron_length 1000
-extracting gene gtfs
-cleaning gene GTFs.
-splitting readthru fusions into composite genes
-building fusion contigs.
[1/3 = 33.3 % done]
[2/3 = 66.7 % done]
[3/3 = 100.0 % done] Done.
CMD: samtools faidx /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa
Execution Time = 0.18 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/fusion_pair_to_mini_genome_join.pl --fusions 046i_bl9_PDAC_AllprepFFPE.fusionreport.tsv --gtf /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/cp_gtf_file_workdir.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf > /tmp/nxf.iLEdUjDiW5/IGV_inputs/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf > /tmp/nxf.iLEdUjDiW5/IGV_inputs/cytoBand.txt
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/cytoband.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/gtf_gene_to_bed.pl /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf > /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed
-parsing GTF file: /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/gtf_gene_to_bed.pl /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.gtf > /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed > /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed > /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/046i_bl9_PDAC_AllprepFFPE.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/046i_bl9_PDAC_AllprepFFPE.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.bed.sorted.bed.gz
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/046i_bl9_PDAC_AllprepFFPE.bed.tabix.ok
Running: samtools faidx /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/merged_contig_fai.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/run_FI_STAR.pl --genome /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa --max_mate_dist 100000 -G /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --CPU 12 --out_prefix 046i_bl9_PDAC_AllprepFFPE.star --out_dir /tmp/nxf.iLEdUjDiW5/fi_workdir --reads "/tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R1.fastp.fastq.gz /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R2.fastp.fastq.gz"
* Running CMD: /opt/conda/bin/STAR --runThreadN 12 --genomeDir /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R1.fastp.fastq.gz /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' --limitBAMsortRAM 47271261705
/opt/conda/bin/STAR-avx2 --runThreadN 12 --genomeDir /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R1.fastp.fastq.gz /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand "gunzip -c" --limitBAMsortRAM 47271261705
STAR version: 2.7.11b compiled: 2024-12-15T08:41:36+0000 :/opt/conda/conda-bld/star_1734251957083/work/source
May 13 13:33:20 ..... started STAR run
May 13 13:33:20 ..... loading genome
May 13 13:35:14 ... generating Suffix Array index
May 13 13:38:28 ... completed Suffix Array index
May 13 13:38:29 ..... processing annotations GTF
May 13 13:38:29 ..... inserting junctions into the genome indices
May 13 13:39:42 ..... started mapping
May 13 13:44:05 ..... finished mapping
May 13 13:44:06 ..... started sorting BAM
May 13 13:44:06 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 046i_bl9_PDAC_AllprepFFPE.star.sortedByCoord.out.bam
* Running CMD: samtools index 046i_bl9_PDAC_AllprepFFPE.star.sortedByCoord.out.bam
Execution Time = 10.77 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/run_FI_STAR.pl --genome /tmp/nxf.iLEdUjDiW5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fa --max_mate_dist 100000 -G /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --CPU 12 --out_prefix 046i_bl9_PDAC_AllprepFFPE.star --out_dir /tmp/nxf.iLEdUjDiW5/fi_workdir --reads "/tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R1.fastp.fastq.gz /tmp/nxf.iLEdUjDiW5/046i_bl9_PDAC_AllprepFFPE_R2.fastp.fastq.gz"
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/run_STAR.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/bam_mark_duplicates.py -i /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.sortedByCoord.out.bam -o /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --remove_dups
13:44:07 : INFO : Done.
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/bam_mark_duplicates.py -i /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.sortedByCoord.out.bam -o /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/mark_dups_reads.index.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf
-parsing /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam
-done parsing /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 6,
'per_id < 96' => 196,
'excessive soft clipping' => 136,
'seq-similar region overlap' => 18,
'small anchor length' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 35,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 188,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 225
};
-writing fusion junction support info.
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: CSF2RA--IL3RA
[1000] -fusion SPANNING read extraction for scaff: ENSG00000290548--GUSBP2
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: ENSG00000290674--SMG1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 1226,
'lacks exon overlap' => 2088
};
Execution Time = 0.01 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/coalesce_junc_n_span.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/fusion_EM_runner.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: 0.000000
EM: Round [1] log likelihood: 0.000000
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/fusion_EM_runner.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/init_EM_adj_counts.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/filter_by_frag_threshs.ok
Running: /opt/conda/share/fusion-inspector-2.10.0-0/util/column_extractions.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /opt/conda/share/fusion-inspector-2.10.0-0/util/column_extractions.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.iLEdUjDiW5/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /opt/conda/share/fusion-inspector-2.10.0-0/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 12 -bT /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa - | samtools sort -@ 12 - -o /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.junction_reads.bam"
[main_samview] fail to read the header from "-".
[W::hts_set_opt] Cannot change block size for this format
samtools sort: failed to read header from "-"
Error: Command 'bash -c "set -eof pipefail; /opt/conda/share/fusion-inspector-2.10.0-0/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 12 -bT /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa - | samtools sort -@ 12 - -o /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.junction_reads.bam"' returned non-zero exit status 1., exit val: 1
Error, command: [ bash -c "set -eof pipefail; /opt/conda/share/fusion-inspector-2.10.0-0/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 12 -bT /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa - | samtools sort -@ 12 - -o /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.junction_reads.bam" ] failed, stack trace: [ st: file:/opt/conda/share/fusion-inspector-2.10.0-0/PyLib/Pipeliner.py, lineno:86
st: file:/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector, lineno:987
st: file:/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector, lineno:1977
]
Traceback (most recent call last):
File "/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector", line 1977, in <module>
FusionInspector().run()
File "/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector", line 1550, in run
pipeliner.run()
File "/opt/conda/share/fusion-inspector-2.10.0-0/PyLib/Pipeliner.py", line 71, in run
cmd.run(checkpoint_dir)
File "/opt/conda/share/fusion-inspector-2.10.0-0/PyLib/Pipeliner.py", line 132, in run
raise RuntimeError(errmsg)
RuntimeError: Error, command: [ bash -c "set -eof pipefail; /opt/conda/share/fusion-inspector-2.10.0-0/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.iLEdUjDiW5/fi_workdir/046i_bl9_PDAC_AllprepFFPE.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 12 -bT /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.fa - | samtools sort -@ 12 - -o /tmp/nxf.iLEdUjDiW5/IGV_inputs/046i_bl9_PDAC_AllprepFFPE.junction_reads.bam" ] failed, stack trace: [ st: file:/opt/conda/share/fusion-inspector-2.10.0-0/PyLib/Pipeliner.py, lineno:86
st: file:/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector, lineno:987
st: file:/opt/conda/share/fusion-inspector-2.10.0-0/FusionInspector, lineno:1977
]
Description of the bug
CC @apeltzer @atrigila
Command used and terminal output
Relevant files
No response
System information
No response