.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-45523c-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/ecb85a2b3acdd057f59f0658c3cda5/.command.log
Size: 60.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-45523c-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/dc6c141c2314e89bd1fd3d7c96f0b9/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/ecb85a2b3acdd057f59f0658c3cda5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/ecb85a2b3acdd057f59f0658c3cda5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/dc6c141c2314e89bd1fd3d7c96f0b9/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/4e83e0291cd79f5844978578fc5def/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf > /tmp/nxf.O1J2x8c046/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf > /tmp/nxf.O1J2x8c046/cytoBand.txt
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.O1J2x8c046/fi_workdir --reads "/tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 03 20:49:37 ..... started STAR run
Jun 03 20:49:37 ..... loading genome
Jun 03 20:51:16 ... generating Suffix Array index
Jun 03 20:55:02 ... completed Suffix Array index
Jun 03 20:55:02 ..... processing annotations GTF
Jun 03 20:55:02 ..... inserting junctions into the genome indices
Jun 03 20:56:03 ..... started mapping
Jun 03 21:55:27 ..... finished mapping
Jun 03 21:55:28 ..... started sorting BAM
Jun 03 21:55:29 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 65.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.O1J2x8c046/fi_workdir --reads "/tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
21:55:36 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1170000]   -done parsing /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'seq-similar region overlap' => 98,
          'small anchor length' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 53,
          'num genes matched < 2' => 12,
          'per_id < 96' => 4571,
          ' ** passed ** ' => 3077,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 21,
          'excessive soft clipping' => 7635,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
          'low complexity anchor region' => 2
        };
-writing fusion junction support info.
Execution Time = 0.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[6000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[83000]   -fusion SPANNING read extraction for scaff: CPSF7--PIEZO2

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[24000]   -fusion SPANNING read extraction for scaff: CPSF7--AP005139.1

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[168000]   -fusion SPANNING read extraction for scaff: DDX5--SMURF2

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[45000]   
[46000]   -fusion SPANNING read extraction for scaff: DHX38--WWOX

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[58000]   
[59000]   -fusion SPANNING read extraction for scaff: ERC1--RASSF7

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[53000]   
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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

[1000]   
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[52000]   
[53000]   
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[55000]   
[56000]   
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[60000]   
[61000]   -fusion SPANNING read extraction for scaff: KIAA1958--NTRK2

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[63000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: LMNTD2--ERC1

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: NAE1--CAPNS2

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
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[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
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[6000]   
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[8000]   
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[13000]   
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[20000]   
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[68000]   
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[70000]   
[71000]   
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[75000]   
[76000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[18000]   
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[20000]   
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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[8000]   
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[29000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[8000]   
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[11000]   
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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[25000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: TXNL4B--CTCF

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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: TXNL4B--CARMIL2

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[72000]   
[73000]   -fusion SPANNING read extraction for scaff: WWP2--MPHOSPH6

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[183000]   
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[202000]   
[203000]   -fusion SPANNING read extraction for scaff: ZFHX3--CNTNAP4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 19027,
          'lacks exon overlap' => 46966
        };
Execution Time = 1.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2786.763736
EM: Round [1] log likelihood: -2786.453495
EM: Round [2] log likelihood: -2786.168151
EM: Round [3] log likelihood: -2785.905189
EM: Round [4] log likelihood: -2785.662421
EM: Round [5] log likelihood: -2785.437939
EM: Round [6] log likelihood: -2785.230063
EM: Round [7] log likelihood: -2785.037310
EM: Round [8] log likelihood: -2784.858363
EM: Round [9] log likelihood: -2784.692052
EM: Round [10] log likelihood: -2784.537328
EM: Round [11] log likelihood: -2784.393250
EM: Round [12] log likelihood: -2784.258972
EM: Round [13] log likelihood: -2784.133728
EM: Round [14] log likelihood: -2784.016826
EM: Round [15] log likelihood: -2783.907638
EM: Round [16] log likelihood: -2783.805591
EM: Round [17] log likelihood: -2783.710164
EM: Round [18] log likelihood: -2783.620879
EM: Round [19] log likelihood: -2783.537301
EM: Round [20] log likelihood: -2783.459028
EM: Round [21] log likelihood: -2783.385693
EM: Round [22] log likelihood: -2783.316956
EM: Round [23] log likelihood: -2783.252506
EM: Round [24] log likelihood: -2783.192054
EM: Round [25] log likelihood: -2783.135334
EM: Round [26] log likelihood: -2783.082100
EM: Round [27] log likelihood: -2783.032123
EM: Round [28] log likelihood: -2782.985191
EM: Round [29] log likelihood: -2782.941109
EM: Round [30] log likelihood: -2782.899694
EM: Round [31] log likelihood: -2782.860776
EM: Round [32] log likelihood: -2782.824197
EM: Round [33] log likelihood: -2782.789810
EM: Round [34] log likelihood: -2782.757478
EM: Round [35] log likelihood: -2782.727073
EM: Round [36] log likelihood: -2782.698476
EM: Round [37] log likelihood: -2782.671575
EM: Round [38] log likelihood: -2782.646267
EM: Round [39] log likelihood: -2782.622453
EM: Round [40] log likelihood: -2782.600044
EM: Round [41] log likelihood: -2782.578953
EM: Round [42] log likelihood: -2782.559102
EM: Round [43] log likelihood: -2782.540415
EM: Round [44] log likelihood: -2782.522822
EM: Round [45] log likelihood: -2782.506258
EM: Round [46] log likelihood: -2782.490662
EM: Round [47] log likelihood: -2782.475975
EM: Round [48] log likelihood: -2782.462144
EM: Round [49] log likelihood: -2782.449118
EM: Round [50] log likelihood: -2782.436849
EM: Round [51] log likelihood: -2782.425293
EM: Round [52] log likelihood: -2782.414407
EM: Round [53] log likelihood: -2782.404153
EM: Round [54] log likelihood: -2782.394492
EM: Round [55] log likelihood: -2782.385391
EM: Round [56] log likelihood: -2782.376816
EM: Round [57] log likelihood: -2782.368736
EM: Round [58] log likelihood: -2782.361124
EM: Round [59] log likelihood: -2782.353950
EM: Round [60] log likelihood: -2782.347191
EM: Round [61] log likelihood: -2782.340821
EM: Round [62] log likelihood: -2782.334818
EM: Round [63] log likelihood: -2782.329161
EM: Round [64] log likelihood: -2782.323830
EM: Round [65] log likelihood: -2782.318806
EM: Round [66] log likelihood: -2782.314070
EM: Round [67] log likelihood: -2782.309607
EM: Round [68] log likelihood: -2782.305401
EM: Round [69] log likelihood: -2782.301436
EM: Round [70] log likelihood: -2782.297699
EM: Round [71] log likelihood: -2782.294177
EM: Round [72] log likelihood: -2782.290856
EM: Round [73] log likelihood: -2782.287727
EM: Round [74] log likelihood: -2782.284777
EM: Round [75] log likelihood: -2782.281996
EM: Round [76] log likelihood: -2782.279374
EM: Round [77] log likelihood: -2782.276903
EM: Round [78] log likelihood: -2782.274574
EM: Round [79] log likelihood: -2782.272378
EM: Round [80] log likelihood: -2782.270308
EM: Round [81] log likelihood: -2782.268357
EM: Round [82] log likelihood: -2782.266517
EM: Round [83] log likelihood: -2782.264783
EM: Round [84] log likelihood: -2782.263148
EM: Round [85] log likelihood: -2782.261607
EM: Round [86] log likelihood: -2782.260154
EM: Round [87] log likelihood: -2782.258784
EM: Round [88] log likelihood: -2782.257493
EM: Round [89] log likelihood: -2782.256275
EM: Round [90] log likelihood: -2782.255128
EM: Round [91] log likelihood: -2782.254046
EM: Round [92] log likelihood: -2782.253025
EM: Round [93] log likelihood: -2782.252064
EM: Round [94] log likelihood: -2782.251157
EM: Round [95] log likelihood: -2782.250302
EM: Round [96] log likelihood: -2782.249496
EM: Round [97] log likelihood: -2782.248736
EM: Round [98] log likelihood: -2782.248020
EM: Round [99] log likelihood: -2782.247344
EM: Round [100] log likelihood: -2782.246708
EM: Round [101] log likelihood: -2782.246107
EM: Round [102] log likelihood: -2782.245541
EM: Round [103] log likelihood: -2782.245007
EM: Round [104] log likelihood: -2782.244504
EM: Round [105] log likelihood: -2782.244030
EM: Round [106] log likelihood: -2782.243583
EM: Round [107] log likelihood: -2782.243161
EM: Round [108] log likelihood: -2782.242763
EM: Round [109] log likelihood: -2782.242389
EM: Round [110] log likelihood: -2782.242035
EM: Round [111] log likelihood: -2782.241702
EM: Round [112] log likelihood: -2782.241388
EM: Round [113] log likelihood: -2782.241092
EM: Round [114] log likelihood: -2782.240812
EM: Round [115] log likelihood: -2782.240549
EM: Round [116] log likelihood: -2782.240301
EM: Round [117] log likelihood: -2782.240067
EM: Round [118] log likelihood: -2782.239846
EM: Round [119] log likelihood: -2782.239638
EM: Round [120] log likelihood: -2782.239442
EM: Round [121] log likelihood: -2782.239257
EM: Round [122] log likelihood: -2782.239082
EM: Round [123] log likelihood: -2782.238918
EM: Round [124] log likelihood: -2782.238763
EM: Round [125] log likelihood: -2782.238617
EM: Round [126] log likelihood: -2782.238479
EM: Round [127] log likelihood: -2782.238349
EM: Round [128] log likelihood: -2782.238226
EM: Round [129] log likelihood: -2782.238111
EM: Round [130] log likelihood: -2782.238002
EM: Round [131] log likelihood: -2782.237899
EM: Round [132] log likelihood: -2782.237803
EM: Stopping iterations at round 132 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/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.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/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.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa > /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.O1J2x8c046/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir
-done, see /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2611.979692
EM: Round [1] log likelihood: -2611.979692
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 241112810
Execution Time = 4.63 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.O1J2x8c046/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.O1J2x8c046/fi_workdir/microH.dat
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.O1J2x8c046/fi_workdir/microH.dat /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.O1J2x8c046/fi_workdir/microH.dat /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.O1J2x8c046 --json_outfile /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.O1J2x8c046 --json_outfile /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1 --html_output /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1 --html_output /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.O1J2x8c046/ctat_genome_lib_build_dir > /tmp/nxf.O1J2x8c046/aih-tih-sc-45523c-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.O1J2x8c046/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory