Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/1b4fd0e161943aac694725cdf45ff3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/bb3651e369458228993af5ebc5bbb0/aih-tih-sc-714733-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/6b/1b4fd0e161943aac694725cdf45ff3/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/bb3651e369458228993af5ebc5bbb0/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/658ff6850018d84300e0d502773c41/aih-tih-sc-714733-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-714733-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-714733-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/cytoBand.txt
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/cytoBand.txt
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-714733-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.gh2FWUWXU7/fi_workdir --reads "/tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:07:07 ..... started STAR run
Jun 08 10:07:07 ..... loading genome
Jun 08 10:09:01 ... generating Suffix Array index
Jun 08 10:12:49 ... completed Suffix Array index
Jun 08 10:12:50 ..... processing annotations GTF
Jun 08 10:12:50 ..... inserting junctions into the genome indices
Jun 08 10:13:54 ..... started mapping
Jun 08 11:24:15 ..... finished mapping
Jun 08 11:24:17 ..... started sorting BAM
Jun 08 11:24:24 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-714733-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-714733-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 77.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-714733-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.gh2FWUWXU7/fi_workdir --reads "/tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:25:53 : INFO : Done.
Execution Time = 1.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.15 minutes. CMD: samtools index /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[14340000] -done parsing /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 792,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 712,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2538,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 798,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
'small anchor length' => 49,
'excessive soft clipping' => 125230,
'num genes matched < 2' => 106,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 24,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 48,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 120,
'seq-similar region overlap' => 26,
'low complexity anchor region' => 108,
'per_id < 96' => 60451,
' ** passed ** ' => 18529,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 315,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
'exons hit < 2' => 40,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1871,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 366
};
-writing fusion junction support info.
Execution Time = 8.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[21000] -fusion SPANNING read extraction for scaff: ABBA01000935.2--CUBN
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[14000] -fusion SPANNING read extraction for scaff: AC068769.1--KLHL6
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[23000] -fusion SPANNING read extraction for scaff: AC090735.1--COL25A1
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[14000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[8000] -fusion SPANNING read extraction for scaff: AC097520.2--GRID2
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[36000] -fusion SPANNING read extraction for scaff: AC132807.2--NAALADL2
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[24000] -fusion SPANNING read extraction for scaff: ACOXL--BCL2L11
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[107000] -fusion SPANNING read extraction for scaff: ADNP--LRRC3-DT
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[47000] -fusion SPANNING read extraction for scaff: AGFG1--AC073065.1
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[14000] -fusion SPANNING read extraction for scaff: AK3--RPS18P6
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[14000] -fusion SPANNING read extraction for scaff: AK3--MTHFD2P1
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[11000] -fusion SPANNING read extraction for scaff: AL139042.1--CNR1
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[766000] -fusion SPANNING read extraction for scaff: AL163952.1--KTN1
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[14000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
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[15000] -fusion SPANNING read extraction for scaff: AL513327.1--LRRC7
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[61000] -fusion SPANNING read extraction for scaff: ANAPC10--ZNF827
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[46000] -fusion SPANNING read extraction for scaff: ARHGAP12--RPL34P19
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[78000] -fusion SPANNING read extraction for scaff: ATL2--HNRNPLL
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[35000] -fusion SPANNING read extraction for scaff: ATP6V1H--SNTG1
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[121000] -fusion SPANNING read extraction for scaff: AUTS2--MAGI2
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[155000] -fusion SPANNING read extraction for scaff: BCAS3--MED13
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[81000] -fusion SPANNING read extraction for scaff: C19orf12--DISP1
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[72000] -fusion SPANNING read extraction for scaff: C19orf12--AC008798.3
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[82000] -fusion SPANNING read extraction for scaff: CACHD1--PDE4B
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[84000] -fusion SPANNING read extraction for scaff: CACHD1--RBAK
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[44000] -fusion SPANNING read extraction for scaff: CBFB--NUTF2
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[42000] -fusion SPANNING read extraction for scaff: CBWD2--AC016745.1
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[26000] -fusion SPANNING read extraction for scaff: CCSER1--GRID2
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[14000] -fusion SPANNING read extraction for scaff: CD2AP--WAKMAR2
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[14000] -fusion SPANNING read extraction for scaff: CD2AP--AL591468.1
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[145000] -fusion SPANNING read extraction for scaff: CD2AP--TNFAIP3
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[32000] -fusion SPANNING read extraction for scaff: CDC73--LINC01031
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[33000] -fusion SPANNING read extraction for scaff: CDR2L--SOX9-AS1
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[797000] -fusion SPANNING read extraction for scaff: COL8A2--KTN1
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[287000] -fusion SPANNING read extraction for scaff: CTNNBIP1--RERE
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[46000] -fusion SPANNING read extraction for scaff: DCAF6--AL603841.1
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[46000] -fusion SPANNING read extraction for scaff: DCAF6--RNA5SP62
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[55000] -fusion SPANNING read extraction for scaff: DIS3L2--ARMC9
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[31000] -fusion SPANNING read extraction for scaff: DIS3L2--AL162400.2
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[19000] -fusion SPANNING read extraction for scaff: DNAJC1--AL035258.1
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[19000] -fusion SPANNING read extraction for scaff: DNAJC1--LINC01432
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[16000] -fusion SPANNING read extraction for scaff: EHD4--CSMD1
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[52000] -fusion SPANNING read extraction for scaff: EHMT1--AC003975.1
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[52000] -fusion SPANNING read extraction for scaff: EHMT1--AC000372.1
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[379000] -fusion SPANNING read extraction for scaff: EIF4G3--NOTCH2NLC
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[109000] -fusion SPANNING read extraction for scaff: EPB41--PHACTR4
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[89000] -fusion SPANNING read extraction for scaff: ESYT1--IKZF4
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[128000] -fusion SPANNING read extraction for scaff: EYA2--NCOA3
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[22000] -fusion SPANNING read extraction for scaff: FAM3C--IMMP2L
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[7000] -fusion SPANNING read extraction for scaff: FBXL12P1--C1D
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[16000] -fusion SPANNING read extraction for scaff: FBXO31--C16orf95
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[15000] -fusion SPANNING read extraction for scaff: FBXO31--AC093519.2
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[51000] -fusion SPANNING read extraction for scaff: FMNL2--AC079790.2
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[13000] -fusion SPANNING read extraction for scaff: FRRS1--PALMD
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[64000] -fusion SPANNING read extraction for scaff: GOLPH3--MTMR12
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[19000] -fusion SPANNING read extraction for scaff: GPD2--LINC01958
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[56000] -fusion SPANNING read extraction for scaff: HEATR5A--PAK1
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[18000] -fusion SPANNING read extraction for scaff: HSCB--KREMEN1
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[46000] -fusion SPANNING read extraction for scaff: HYDIN--VAC14
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[29000] -fusion SPANNING read extraction for scaff: IFNAR1--OLIG1
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[58000] -fusion SPANNING read extraction for scaff: IQCB1--POLQ
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[48000] -fusion SPANNING read extraction for scaff: KIF2A--IPO11
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[26000] -fusion SPANNING read extraction for scaff: LCLAT1--AC106870.3
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[8000] -fusion SPANNING read extraction for scaff: LINC00265--SUGCT
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[765000] -fusion SPANNING read extraction for scaff: LINC00520--KTN1
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[7000] -fusion SPANNING read extraction for scaff: LINC01812--C1D
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[112000] -fusion SPANNING read extraction for scaff: LRP5--ALG1L9P
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[111000] -fusion SPANNING read extraction for scaff: LRP5--AC004923.2
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[111000] -fusion SPANNING read extraction for scaff: LRP5--LINC02754
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[111000] -fusion SPANNING read extraction for scaff: LRP5--RPS3AP40
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[47000] -fusion SPANNING read extraction for scaff: LYPLA1--XKR4
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[115000] -fusion SPANNING read extraction for scaff: MAN2B1--CACNA1A
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[60000] -fusion SPANNING read extraction for scaff: MBD1--SLC14A2
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[59000] -fusion SPANNING read extraction for scaff: MUS81--CTSW
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[319000] -fusion SPANNING read extraction for scaff: NCOR2--AC073592.4
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[319000] -fusion SPANNING read extraction for scaff: NCOR2--AC073593.1
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[17000] -fusion SPANNING read extraction for scaff: NRXN1--WDPCP
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[198000] -fusion SPANNING read extraction for scaff: PABPN1--GRM5
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[105000] -fusion SPANNING read extraction for scaff: PACS1--MUS81
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[82000] -fusion SPANNING read extraction for scaff: PACS1--CTSW
[1000]
[2000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[2000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[3000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[3000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[4000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[4000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[822000] -fusion SPANNING read extraction for scaff: PELI2--KTN1
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[80000] -fusion SPANNING read extraction for scaff: PELI2--MIS18BP1
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[297000] -fusion SPANNING read extraction for scaff: PFKL--TRPM2
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[28000] -fusion SPANNING read extraction for scaff: PIP4K2B--AC015943.1
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[28000] -fusion SPANNING read extraction for scaff: PIP4K2B--AC005951.1
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[64000] -fusion SPANNING read extraction for scaff: PIP5K1A--PLGRKT
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[73000] -fusion SPANNING read extraction for scaff: PIP5K1A--CD274
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[34000] -fusion SPANNING read extraction for scaff: PRIM2--CUBN
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[8000] -fusion SPANNING read extraction for scaff: PSG8--CD177
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[140000] -fusion SPANNING read extraction for scaff: PTK2--AC048380.1
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[52000] -fusion SPANNING read extraction for scaff: RALBP1--RNA5SP443
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[53000] -fusion SPANNING read extraction for scaff: RALBP1--AC003070.2
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[159000] -fusion SPANNING read extraction for scaff: RARA--STARD3
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[5000] -fusion SPANNING read extraction for scaff: REM2--PCDH11X
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[57000] -fusion SPANNING read extraction for scaff: SATB1--NAALADL2
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[34000] -fusion SPANNING read extraction for scaff: SEMA4D--SHC3
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[42000] -fusion SPANNING read extraction for scaff: SHROOM3--CCDC158
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[216000] -fusion SPANNING read extraction for scaff: SMG1--AC002310.3
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[225000] -fusion SPANNING read extraction for scaff: SMG1--ZNF764
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[96000] -fusion SPANNING read extraction for scaff: SMURF2--GPRC5C
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[79000] -fusion SPANNING read extraction for scaff: SP100--FBXO36
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[58000] -fusion SPANNING read extraction for scaff: SPDL1--DOCK2
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[34000] -fusion SPANNING read extraction for scaff: SPIRE2--HFM1
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[35000] -fusion SPANNING read extraction for scaff: SPIRE2--CDC7
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[125000] -fusion SPANNING read extraction for scaff: SPON1--LINC02548
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[125000] -fusion SPANNING read extraction for scaff: SPON1--LINC02683
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[86000] -fusion SPANNING read extraction for scaff: STRBP--DENND1A
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[144000] -fusion SPANNING read extraction for scaff: TDRD10--IGL@-ext
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[68000] -fusion SPANNING read extraction for scaff: TEX2--RBFOX3
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[124000] -fusion SPANNING read extraction for scaff: THRAP3--AL163952.1
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[51000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[21000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[592000] -fusion SPANNING read extraction for scaff: TPM3--ADAR
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[75000] -fusion SPANNING read extraction for scaff: TTLL4--PLCD4
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[39000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[171000] -fusion SPANNING read extraction for scaff: UBAP2L--SPRR2D
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[48000] -fusion SPANNING read extraction for scaff: VEZT--FGD6
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[17000] -fusion SPANNING read extraction for scaff: WDPCP--NRXN1
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[458000] -fusion SPANNING read extraction for scaff: WNK1--SLC45A4
[1000]
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[39000] -fusion SPANNING read extraction for scaff: ZBTB2P1--FHAD1
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[99000] -fusion SPANNING read extraction for scaff: ZBTB8OS--YARS1
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[50000] -fusion SPANNING read extraction for scaff: ZDHHC11--BRD9
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[47000] -fusion SPANNING read extraction for scaff: ZNF326--GCLC
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 128203,
'seq similar region alignment' => 29202
};
Execution Time = 24.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -47747.287085
EM: Round [1] log likelihood: -47735.232145
EM: Round [2] log likelihood: -47735.030733
EM: Round [3] log likelihood: -47734.942678
EM: Round [4] log likelihood: -47734.872474
EM: Round [5] log likelihood: -47734.809478
EM: Round [6] log likelihood: -47734.750891
EM: Round [7] log likelihood: -47734.695812
EM: Round [8] log likelihood: -47734.643831
EM: Round [9] log likelihood: -47734.594684
EM: Round [10] log likelihood: -47734.548155
EM: Round [11] log likelihood: -47734.504056
EM: Round [12] log likelihood: -47734.462219
EM: Round [13] log likelihood: -47734.422492
EM: Round [14] log likelihood: -47734.384734
EM: Round [15] log likelihood: -47734.348820
EM: Round [16] log likelihood: -47734.314631
EM: Round [17] log likelihood: -47734.282062
EM: Round [18] log likelihood: -47734.251014
EM: Round [19] log likelihood: -47734.221396
EM: Round [20] log likelihood: -47734.193123
EM: Round [21] log likelihood: -47734.166120
EM: Round [22] log likelihood: -47734.140313
EM: Round [23] log likelihood: -47734.115636
EM: Round [24] log likelihood: -47734.092027
EM: Round [25] log likelihood: -47734.069428
EM: Round [26] log likelihood: -47734.047786
EM: Round [27] log likelihood: -47734.027049
EM: Round [28] log likelihood: -47734.007172
EM: Round [29] log likelihood: -47733.988110
EM: Round [30] log likelihood: -47733.969821
EM: Round [31] log likelihood: -47733.952269
EM: Round [32] log likelihood: -47733.935415
EM: Round [33] log likelihood: -47733.919227
EM: Round [34] log likelihood: -47733.903672
EM: Round [35] log likelihood: -47733.888720
EM: Round [36] log likelihood: -47733.874344
EM: Round [37] log likelihood: -47733.860515
EM: Round [38] log likelihood: -47733.847210
EM: Round [39] log likelihood: -47733.834404
EM: Round [40] log likelihood: -47733.822075
EM: Round [41] log likelihood: -47733.810202
EM: Round [42] log likelihood: -47733.798764
EM: Round [43] log likelihood: -47733.787743
EM: Round [44] log likelihood: -47733.777120
EM: Round [45] log likelihood: -47733.766879
EM: Round [46] log likelihood: -47733.757004
EM: Round [47] log likelihood: -47733.747478
EM: Round [48] log likelihood: -47733.738288
EM: Round [49] log likelihood: -47733.729420
EM: Round [50] log likelihood: -47733.720860
EM: Round [51] log likelihood: -47733.712595
EM: Round [52] log likelihood: -47733.704616
EM: Round [53] log likelihood: -47733.696908
EM: Round [54] log likelihood: -47733.689463
EM: Round [55] log likelihood: -47733.682269
EM: Round [56] log likelihood: -47733.675318
EM: Round [57] log likelihood: -47733.668599
EM: Round [58] log likelihood: -47733.662103
EM: Round [59] log likelihood: -47733.655823
EM: Round [60] log likelihood: -47733.649749
EM: Round [61] log likelihood: -47733.643875
EM: Round [62] log likelihood: -47733.638193
EM: Round [63] log likelihood: -47733.632695
EM: Round [64] log likelihood: -47733.627375
EM: Round [65] log likelihood: -47733.622227
EM: Round [66] log likelihood: -47733.617244
EM: Round [67] log likelihood: -47733.612420
EM: Round [68] log likelihood: -47733.607750
EM: Round [69] log likelihood: -47733.603227
EM: Round [70] log likelihood: -47733.598848
EM: Round [71] log likelihood: -47733.594607
EM: Round [72] log likelihood: -47733.590498
EM: Round [73] log likelihood: -47733.586518
EM: Round [74] log likelihood: -47733.582662
EM: Round [75] log likelihood: -47733.578926
EM: Round [76] log likelihood: -47733.575306
EM: Round [77] log likelihood: -47733.571797
EM: Round [78] log likelihood: -47733.568396
EM: Round [79] log likelihood: -47733.565099
EM: Round [80] log likelihood: -47733.561904
EM: Round [81] log likelihood: -47733.558805
EM: Round [82] log likelihood: -47733.555801
EM: Round [83] log likelihood: -47733.552888
EM: Round [84] log likelihood: -47733.550063
EM: Round [85] log likelihood: -47733.547324
EM: Round [86] log likelihood: -47733.544667
EM: Round [87] log likelihood: -47733.542089
EM: Round [88] log likelihood: -47733.539589
EM: Round [89] log likelihood: -47733.537164
EM: Round [90] log likelihood: -47733.534811
EM: Round [91] log likelihood: -47733.532528
EM: Round [92] log likelihood: -47733.530313
EM: Round [93] log likelihood: -47733.528164
EM: Round [94] log likelihood: -47733.526078
EM: Round [95] log likelihood: -47733.524054
EM: Round [96] log likelihood: -47733.522089
EM: Round [97] log likelihood: -47733.520182
EM: Round [98] log likelihood: -47733.518332
EM: Round [99] log likelihood: -47733.516535
EM: Round [100] log likelihood: -47733.514792
EM: Round [101] log likelihood: -47733.513099
EM: Round [102] log likelihood: -47733.511455
EM: Round [103] log likelihood: -47733.509860
EM: Round [104] log likelihood: -47733.508311
EM: Round [105] log likelihood: -47733.506807
EM: Round [106] log likelihood: -47733.505346
EM: Round [107] log likelihood: -47733.503928
EM: Round [108] log likelihood: -47733.502551
EM: Round [109] log likelihood: -47733.501214
EM: Round [110] log likelihood: -47733.499916
EM: Round [111] log likelihood: -47733.498654
EM: Round [112] log likelihood: -47733.497430
EM: Round [113] log likelihood: -47733.496240
EM: Round [114] log likelihood: -47733.495085
EM: Round [115] log likelihood: -47733.493963
EM: Round [116] log likelihood: -47733.492873
EM: Round [117] log likelihood: -47733.491814
EM: Round [118] log likelihood: -47733.490785
EM: Round [119] log likelihood: -47733.489786
EM: Round [120] log likelihood: -47733.488816
EM: Round [121] log likelihood: -47733.487873
EM: Round [122] log likelihood: -47733.486957
EM: Round [123] log likelihood: -47733.486068
EM: Round [124] log likelihood: -47733.485203
EM: Round [125] log likelihood: -47733.484364
EM: Round [126] log likelihood: -47733.483548
EM: Round [127] log likelihood: -47733.482755
EM: Round [128] log likelihood: -47733.481985
EM: Round [129] log likelihood: -47733.481237
EM: Round [130] log likelihood: -47733.480509
EM: Round [131] log likelihood: -47733.479803
EM: Round [132] log likelihood: -47733.479117
EM: Round [133] log likelihood: -47733.478449
EM: Round [134] log likelihood: -47733.477801
EM: Round [135] log likelihood: -47733.477172
EM: Round [136] log likelihood: -47733.476559
EM: Round [137] log likelihood: -47733.475965
EM: Round [138] log likelihood: -47733.475387
EM: Round [139] log likelihood: -47733.474825
EM: Round [140] log likelihood: -47733.474279
EM: Round [141] log likelihood: -47733.473749
EM: Round [142] log likelihood: -47733.473234
EM: Round [143] log likelihood: -47733.472733
EM: Round [144] log likelihood: -47733.472246
EM: Round [145] log likelihood: -47733.471773
EM: Round [146] log likelihood: -47733.471313
EM: Round [147] log likelihood: -47733.470866
EM: Round [148] log likelihood: -47733.470432
EM: Round [149] log likelihood: -47733.470010
EM: Round [150] log likelihood: -47733.469599
EM: Round [151] log likelihood: -47733.469201
EM: Round [152] log likelihood: -47733.468813
EM: Round [153] log likelihood: -47733.468436
EM: Round [154] log likelihood: -47733.468070
EM: Round [155] log likelihood: -47733.467714
EM: Round [156] log likelihood: -47733.467369
EM: Round [157] log likelihood: -47733.467032
EM: Round [158] log likelihood: -47733.466706
EM: Round [159] log likelihood: -47733.466388
EM: Round [160] log likelihood: -47733.466079
EM: Round [161] log likelihood: -47733.465779
EM: Round [162] log likelihood: -47733.465488
EM: Round [163] log likelihood: -47733.465204
EM: Round [164] log likelihood: -47733.464929
EM: Round [165] log likelihood: -47733.464661
EM: Round [166] log likelihood: -47733.464401
EM: Round [167] log likelihood: -47733.464148
EM: Round [168] log likelihood: -47733.463902
EM: Round [169] log likelihood: -47733.463662
EM: Round [170] log likelihood: -47733.463430
EM: Round [171] log likelihood: -47733.463204
EM: Round [172] log likelihood: -47733.462984
EM: Round [173] log likelihood: -47733.462771
EM: Round [174] log likelihood: -47733.462563
EM: Round [175] log likelihood: -47733.462362
EM: Round [176] log likelihood: -47733.462166
EM: Round [177] log likelihood: -47733.461975
EM: Round [178] log likelihood: -47733.461790
EM: Round [179] log likelihood: -47733.461610
EM: Round [180] log likelihood: -47733.461434
EM: Round [181] log likelihood: -47733.461264
EM: Round [182] log likelihood: -47733.461099
EM: Round [183] log likelihood: -47733.460938
EM: Round [184] log likelihood: -47733.460781
EM: Round [185] log likelihood: -47733.460629
EM: Round [186] log likelihood: -47733.460482
EM: Round [187] log likelihood: -47733.460338
EM: Round [188] log likelihood: -47733.460198
EM: Round [189] log likelihood: -47733.460063
EM: Round [190] log likelihood: -47733.459931
EM: Round [191] log likelihood: -47733.459802
EM: Round [192] log likelihood: -47733.459678
EM: Round [193] log likelihood: -47733.459556
EM: Round [194] log likelihood: -47733.459439
EM: Round [195] log likelihood: -47733.459324
EM: Round [196] log likelihood: -47733.459213
EM: Round [197] log likelihood: -47733.459104
EM: Round [198] log likelihood: -47733.458999
EM: Round [199] log likelihood: -47733.458897
EM: Round [200] log likelihood: -47733.458797
EM: Stopping iterations at round 200 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/aih-tih-sc-714733-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.15 minutes. CMD: samtools index /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 3.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.Pfam.gff3
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa > /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir
-done, see /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -46108.609481
EM: Round [1] log likelihood: -46105.024807
EM: Round [2] log likelihood: -46105.020683
EM: Round [3] log likelihood: -46105.020673
EM: Stopping iterations at round 3 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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296727647
Execution Time = 5.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/fi_workdir/microH.dat
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gtf > /tmp/nxf.gh2FWUWXU7/fi_workdir/microH.dat
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.gh2FWUWXU7/fi_workdir/microH.dat /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/fi_workdir/microH.dat /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.gh2FWUWXU7 --json_outfile /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-714733-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.gh2FWUWXU7 --json_outfile /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-714733-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.gh2FWUWXU7/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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-714733-R1_A23YTGFLT4_1 --html_output /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.08 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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-714733-R1_A23YTGFLT4_1 --html_output /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-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.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000243531.1]
WARNING, no entry stored in dbm for [ENSG00000271977.1]
WARNING, no entry stored in dbm for [ENSG00000283436.1]
WARNING, no entry stored in dbm for [ENSG00000283436.1]
WARNING, no entry stored in dbm for [ENSG00000255411.3]
WARNING, no entry stored in dbm for [ENSG00000255411.3]
WARNING, no entry stored in dbm for [ENSG00000255411.3]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000274840.4]
WARNING, no entry stored in dbm for [ENSG00000274840.4]
WARNING, no entry stored in dbm for [ENSG00000274840.4]
WARNING, no entry stored in dbm for [ENSG00000188185.13]
WARNING, no entry stored in dbm for [ENSG00000188185.13]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000267762.1]
WARNING, no entry stored in dbm for [ENSG00000267762.1]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000229172.1]
WARNING, no entry stored in dbm for [ENSG00000287393.1]
WARNING, no entry stored in dbm for [ENSG00000251637.6]
WARNING, no entry stored in dbm for [ENSG00000251637.6]
WARNING, no entry stored in dbm for [ENSG00000251637.6]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000254850.2]
WARNING, no entry stored in dbm for [ENSG00000248671.8]
WARNING, no entry stored in dbm for [ENSG00000248671.8]
WARNING, no entry stored in dbm for [ENSG00000248671.8]
WARNING, no entry stored in dbm for [ENSG00000229225.1]
WARNING, no entry stored in dbm for [ENSG00000225313.5]
WARNING, no entry stored in dbm for [ENSG00000225313.5]
WARNING, no entry stored in dbm for [ENSG00000237499.7]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000229356.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000234997.2]
WARNING, no entry stored in dbm for [ENSG00000234997.2]
WARNING, no entry stored in dbm for [ENSG00000234997.2]
WARNING, no entry stored in dbm for [ENSG00000234997.2]
WARNING, no entry stored in dbm for [ENSG00000286234.1]
WARNING, no entry stored in dbm for [ENSG00000286234.1]
WARNING, no entry stored in dbm for [ENSG00000253784.1]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000232077.2]
WARNING, no entry stored in dbm for [ENSG00000234862.1]
WARNING, no entry stored in dbm for [ENSG00000288036.1]
WARNING, no entry stored in dbm for [ENSG00000237013.1]
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.gh2FWUWXU7/ctat_genome_lib_build_dir > /tmp/nxf.gh2FWUWXU7/aih-tih-sc-714733-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.gh2FWUWXU7/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory