Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c4fa8ad201d4ae4b80f1892b936ead/659_bGW-T1-TRNA-1_A23MVY2LT4_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/5a/5ca2fb259dea7c7262b49d8fb5974c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/5ca2fb259dea7c7262b49d8fb5974c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c4fa8ad201d4ae4b80f1892b936ead/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/9bef0f0528c82184faf6f023df05d8/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusionreport.tsv --gtf /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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 659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusionreport.tsv --gtf /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/cytoBand.txt
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed
-parsing GTF file: /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1.star --out_dir /tmp/nxf.zto05XNcdp/fi_workdir --reads "/tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zto05XNcdp/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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:16:01 ..... started STAR run
Jun 08 10:16:01 ..... loading genome
Jun 08 10:17:59 ... generating Suffix Array index
Jun 08 10:22:16 ... completed Suffix Array index
Jun 08 10:22:17 ..... processing annotations GTF
Jun 08 10:22:17 ..... inserting junctions into the genome indices
Jun 08 10:23:28 ..... started mapping
Jun 08 12:13:10 ..... finished mapping
Jun 08 12:13:13 ..... started sorting BAM
Jun 08 12:13:14 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
Execution Time = 117.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1.star --out_dir /tmp/nxf.zto05XNcdp/fi_workdir --reads "/tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
12:13:28 : INFO : Done.
Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf
-parsing /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam
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[2120000] -done parsing /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 166,
'low complexity anchor region' => 7,
' ** passed ** ' => 4642,
'exons hit < 2' => 106,
'seq-similar region overlap' => 45,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 24,
'per_id < 96' => 9950,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 238,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 20,
'small anchor length' => 3,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 229,
'excessive soft clipping' => 14031
};
-writing fusion junction support info.
Execution Time = 1.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[360000] -fusion SPANNING read extraction for scaff: DLG5--CTSLP1
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[98000] -fusion SPANNING read extraction for scaff: GPRC5A--RFC1
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[80000] -fusion SPANNING read extraction for scaff: JMJD1C--LINC00841
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[80000] -fusion SPANNING read extraction for scaff: JMJD1C--AL137026.2
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[29000] -fusion SPANNING read extraction for scaff: NDUFA9--C12orf4
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[3000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[3000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[49000] -fusion SPANNING read extraction for scaff: PKP2--ASS1P14
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[69000] -fusion SPANNING read extraction for scaff: POLR2E--KEAP1
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[102000] -fusion SPANNING read extraction for scaff: PTPRK--RSPO3
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[98000] -fusion SPANNING read extraction for scaff: RFC1--GPRC5A
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[108000] -fusion SPANNING read extraction for scaff: SLC5A3--RUNX1
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[53000] -fusion SPANNING read extraction for scaff: SULT1B1--TBC1D1
[1000]
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[12000] -fusion SPANNING read extraction for scaff: SULT1B1--AC098680.2
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[20000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[20000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
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[1000]
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[12000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[174000] -fusion SPANNING read extraction for scaff: TYK2--SBNO2
[1000]
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[60000] -fusion SPANNING read extraction for scaff: WDR19--ATP8A1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 2523,
'lacks exon overlap' => 13407
};
Execution Time = 3.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4403.920367
EM: Round [1] log likelihood: -4388.174926
EM: Round [2] log likelihood: -4388.069941
EM: Round [3] log likelihood: -4388.051635
EM: Round [4] log likelihood: -4388.035870
EM: Round [5] log likelihood: -4388.021045
EM: Round [6] log likelihood: -4388.007022
EM: Round [7] log likelihood: -4387.993743
EM: Round [8] log likelihood: -4387.981159
EM: Round [9] log likelihood: -4387.969225
EM: Round [10] log likelihood: -4387.957901
EM: Round [11] log likelihood: -4387.947150
EM: Round [12] log likelihood: -4387.936936
EM: Round [13] log likelihood: -4387.927228
EM: Round [14] log likelihood: -4387.917996
EM: Round [15] log likelihood: -4387.909213
EM: Round [16] log likelihood: -4387.900853
EM: Round [17] log likelihood: -4387.892893
EM: Round [18] log likelihood: -4387.885310
EM: Round [19] log likelihood: -4387.878084
EM: Round [20] log likelihood: -4387.871196
EM: Round [21] log likelihood: -4387.864628
EM: Round [22] log likelihood: -4387.858363
EM: Round [23] log likelihood: -4387.852385
EM: Round [24] log likelihood: -4387.846680
EM: Round [25] log likelihood: -4387.841234
EM: Round [26] log likelihood: -4387.836033
EM: Round [27] log likelihood: -4387.831065
EM: Round [28] log likelihood: -4387.826320
EM: Round [29] log likelihood: -4387.821785
EM: Round [30] log likelihood: -4387.817451
EM: Round [31] log likelihood: -4387.813307
EM: Round [32] log likelihood: -4387.809346
EM: Round [33] log likelihood: -4387.805558
EM: Round [34] log likelihood: -4387.801935
EM: Round [35] log likelihood: -4387.798469
EM: Round [36] log likelihood: -4387.795152
EM: Round [37] log likelihood: -4387.791979
EM: Round [38] log likelihood: -4387.788942
EM: Round [39] log likelihood: -4387.786036
EM: Round [40] log likelihood: -4387.783253
EM: Round [41] log likelihood: -4387.780589
EM: Round [42] log likelihood: -4387.778039
EM: Round [43] log likelihood: -4387.775596
EM: Round [44] log likelihood: -4387.773257
EM: Round [45] log likelihood: -4387.771016
EM: Round [46] log likelihood: -4387.768870
EM: Round [47] log likelihood: -4387.766814
EM: Round [48] log likelihood: -4387.764844
EM: Round [49] log likelihood: -4387.762957
EM: Round [50] log likelihood: -4387.761148
EM: Round [51] log likelihood: -4387.759415
EM: Round [52] log likelihood: -4387.757754
EM: Round [53] log likelihood: -4387.756162
EM: Round [54] log likelihood: -4387.754636
EM: Round [55] log likelihood: -4387.753174
EM: Round [56] log likelihood: -4387.751772
EM: Round [57] log likelihood: -4387.750427
EM: Round [58] log likelihood: -4387.749139
EM: Round [59] log likelihood: -4387.747903
EM: Round [60] log likelihood: -4387.746718
EM: Round [61] log likelihood: -4387.745582
EM: Round [62] log likelihood: -4387.744493
EM: Round [63] log likelihood: -4387.743448
EM: Round [64] log likelihood: -4387.742446
EM: Round [65] log likelihood: -4387.741485
EM: Round [66] log likelihood: -4387.740564
EM: Round [67] log likelihood: -4387.739680
EM: Round [68] log likelihood: -4387.738832
EM: Round [69] log likelihood: -4387.738019
EM: Round [70] log likelihood: -4387.737239
EM: Round [71] log likelihood: -4387.736490
EM: Round [72] log likelihood: -4387.735772
EM: Round [73] log likelihood: -4387.735084
EM: Round [74] log likelihood: -4387.734423
EM: Round [75] log likelihood: -4387.733789
EM: Round [76] log likelihood: -4387.733181
EM: Round [77] log likelihood: -4387.732598
EM: Round [78] log likelihood: -4387.732038
EM: Round [79] log likelihood: -4387.731501
EM: Round [80] log likelihood: -4387.730985
EM: Round [81] log likelihood: -4387.730491
EM: Round [82] log likelihood: -4387.730017
EM: Round [83] log likelihood: -4387.729561
EM: Round [84] log likelihood: -4387.729124
EM: Round [85] log likelihood: -4387.728705
EM: Round [86] log likelihood: -4387.728303
EM: Round [87] log likelihood: -4387.727917
EM: Round [88] log likelihood: -4387.727546
EM: Round [89] log likelihood: -4387.727191
EM: Round [90] log likelihood: -4387.726850
EM: Round [91] log likelihood: -4387.726522
EM: Round [92] log likelihood: -4387.726208
EM: Round [93] log likelihood: -4387.725907
EM: Round [94] log likelihood: -4387.725617
EM: Round [95] log likelihood: -4387.725339
EM: Round [96] log likelihood: -4387.725073
EM: Round [97] log likelihood: -4387.724817
EM: Round [98] log likelihood: -4387.724572
EM: Round [99] log likelihood: -4387.724336
EM: Round [100] log likelihood: -4387.724110
EM: Round [101] log likelihood: -4387.723893
EM: Round [102] log likelihood: -4387.723684
EM: Round [103] log likelihood: -4387.723484
EM: Round [104] log likelihood: -4387.723292
EM: Round [105] log likelihood: -4387.723108
EM: Round [106] log likelihood: -4387.722931
EM: Round [107] log likelihood: -4387.722761
EM: Round [108] log likelihood: -4387.722599
EM: Round [109] log likelihood: -4387.722442
EM: Round [110] log likelihood: -4387.722292
EM: Round [111] log likelihood: -4387.722148
EM: Round [112] log likelihood: -4387.722010
EM: Round [113] log likelihood: -4387.721877
EM: Round [114] log likelihood: -4387.721750
EM: Round [115] log likelihood: -4387.721627
EM: Round [116] log likelihood: -4387.721510
EM: Round [117] log likelihood: -4387.721397
EM: Round [118] log likelihood: -4387.721289
EM: Round [119] log likelihood: -4387.721185
EM: Round [120] log likelihood: -4387.721086
EM: Stopping iterations at round 120 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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam into /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.Pfam.gff3 > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.Pfam.gff3 > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa > /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir
-done, see /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4079.566636
EM: Round [1] log likelihood: -4071.779836
EM: Round [2] log likelihood: -4071.775656
EM: Round [3] log likelihood: -4071.775655
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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz: 295367110
Execution Time = 6.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa --gtf /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fa --gtf /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.gtf > /tmp/nxf.zto05XNcdp/fi_workdir/microH.dat
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.zto05XNcdp/fi_workdir/microH.dat /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/fi_workdir/microH.dat /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zto05XNcdp --json_outfile /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zto05XNcdp --json_outfile /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1
Running: touch /tmp/nxf.zto05XNcdp/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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1 --html_output /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_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.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_A23MVY2LT4_1 --html_output /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000236417.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zto05XNcdp/ctat_genome_lib_build_dir > /tmp/nxf.zto05XNcdp/659_bGW-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.zto05XNcdp/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory