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/a5/8792c6f76125bb90af398990f5d144/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/8792c6f76125bb90af398990f5d144/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/c0f913f67bc3e41afabf49c300df27/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/c0f913f67bc3e41afabf49c300df27/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/26533f422521c2b4cc01d105fad534/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/cytoBand.txt
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed
-parsing GTF file: /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star --out_dir /tmp/nxf.Q3SoObmB84/fi_workdir --reads "/tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:57:45 ..... started STAR run
Jun 08 09:57:45 ..... loading genome
Jun 08 09:59:27 ... generating Suffix Array index
Jun 08 10:03:18 ... completed Suffix Array index
Jun 08 10:03:18 ..... processing annotations GTF
Jun 08 10:03:18 ..... inserting junctions into the genome indices
Jun 08 10:04:19 ..... started mapping
Jun 08 11:03:06 ..... finished mapping
Jun 08 11:03:07 ..... started sorting BAM
Jun 08 11:03:09 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.sortedByCoord.out.bam
Execution Time = 65.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star --out_dir /tmp/nxf.Q3SoObmB84/fi_workdir --reads "/tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:03:34 : INFO : Done.
Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf
-parsing /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
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[4800000] -done parsing /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 161,
'seq-similar region overlap' => 33,
'low complexity anchor region' => 66,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
' ** passed ** ' => 169509,
'small anchor length' => 952,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 17,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'num genes matched < 2' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 548,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 166,
'excessive soft clipping' => 31698,
'per_id < 96' => 18038,
'exons hit < 2' => 30,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 58
};
-writing fusion junction support info.
Execution Time = 2.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[387000] -fusion SPANNING read extraction for scaff: AC004951.2--COBL
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[109000] -fusion SPANNING read extraction for scaff: COBL--NPC1L1
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[11000] -fusion SPANNING read extraction for scaff: EFL1--GOLGA6L11P
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[49000] -fusion SPANNING read extraction for scaff: ESYT2--NCAPG2
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[19000] -fusion SPANNING read extraction for scaff: LANCL2--AC011228.1
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[17000] -fusion SPANNING read extraction for scaff: LANCL2--RNU6-1125P
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[861000] -fusion SPANNING read extraction for scaff: MIR34AHG--QKI
[1000]
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[39000]
[40000]
[41000]
[42000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
[1000]
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[6000]
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[9000]
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[38000]
[39000]
[40000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
[1000]
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[6000]
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[9000]
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[38000]
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[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
[1000]
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[6000]
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[78000]
[79000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
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[70000]
[71000]
[72000]
[73000]
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[76000]
[77000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
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[81000]
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[83000]
[84000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
[1000]
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[67000]
[68000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
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[47000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
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[33000]
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[35000]
[36000]
[37000]
[38000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[40000]
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[47000]
[48000]
[49000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
[1000]
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[71000]
[72000]
[73000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
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[42000]
[43000]
[44000]
[45000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
[1000]
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[65000]
[66000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[556000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[327000] -fusion SPANNING read extraction for scaff: PMS2P1--AC004951.2
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[110000] -fusion SPANNING read extraction for scaff: RERE--CAMTA1
[1000]
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[31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
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[10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[33000] -fusion SPANNING read extraction for scaff: YARS1--CDC45
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[608000] -fusion SPANNING read extraction for scaff: YKT6--COBL
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 280313,
'lacks exon overlap' => 45646
};
Execution Time = 6.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -31484.524473
EM: Round [1] log likelihood: -31482.387083
EM: Round [2] log likelihood: -31481.861258
EM: Round [3] log likelihood: -31481.591336
EM: Round [4] log likelihood: -31481.421146
EM: Round [5] log likelihood: -31481.307347
EM: Round [6] log likelihood: -31481.229138
EM: Round [7] log likelihood: -31481.174400
EM: Round [8] log likelihood: -31481.135537
EM: Round [9] log likelihood: -31481.107590
EM: Round [10] log likelihood: -31481.087236
EM: Round [11] log likelihood: -31481.072205
EM: Round [12] log likelihood: -31481.060928
EM: Round [13] log likelihood: -31481.052306
EM: Round [14] log likelihood: -31481.045569
EM: Round [15] log likelihood: -31481.040174
EM: Round [16] log likelihood: -31481.035734
EM: Round [17] log likelihood: -31481.031975
EM: Round [18] log likelihood: -31481.028703
EM: Round [19] log likelihood: -31481.025778
EM: Round [20] log likelihood: -31481.023103
EM: Round [21] log likelihood: -31481.020607
EM: Round [22] log likelihood: -31481.018239
EM: Round [23] log likelihood: -31481.015963
EM: Round [24] log likelihood: -31481.013753
EM: Round [25] log likelihood: -31481.011592
EM: Round [26] log likelihood: -31481.009467
EM: Round [27] log likelihood: -31481.007367
EM: Round [28] log likelihood: -31481.005287
EM: Round [29] log likelihood: -31481.003221
EM: Round [30] log likelihood: -31481.001166
EM: Round [31] log likelihood: -31480.999120
EM: Round [32] log likelihood: -31480.997081
EM: Round [33] log likelihood: -31480.995047
EM: Round [34] log likelihood: -31480.993019
EM: Round [35] log likelihood: -31480.990994
EM: Round [36] log likelihood: -31480.988974
EM: Round [37] log likelihood: -31480.986956
EM: Round [38] log likelihood: -31480.984942
EM: Round [39] log likelihood: -31480.982931
EM: Round [40] log likelihood: -31480.980922
EM: Round [41] log likelihood: -31480.978916
EM: Round [42] log likelihood: -31480.976913
EM: Round [43] log likelihood: -31480.974913
EM: Round [44] log likelihood: -31480.972915
EM: Round [45] log likelihood: -31480.970920
EM: Round [46] log likelihood: -31480.968927
EM: Round [47] log likelihood: -31480.966937
EM: Round [48] log likelihood: -31480.964950
EM: Round [49] log likelihood: -31480.962964
EM: Round [50] log likelihood: -31480.960982
EM: Round [51] log likelihood: -31480.959002
EM: Round [52] log likelihood: -31480.957024
EM: Round [53] log likelihood: -31480.955049
EM: Round [54] log likelihood: -31480.953076
EM: Round [55] log likelihood: -31480.951106
EM: Round [56] log likelihood: -31480.949139
EM: Round [57] log likelihood: -31480.947173
EM: Round [58] log likelihood: -31480.945210
EM: Round [59] log likelihood: -31480.943250
EM: Round [60] log likelihood: -31480.941292
EM: Round [61] log likelihood: -31480.939337
EM: Round [62] log likelihood: -31480.937384
EM: Round [63] log likelihood: -31480.935433
EM: Round [64] log likelihood: -31480.933485
EM: Round [65] log likelihood: -31480.931539
EM: Round [66] log likelihood: -31480.929595
EM: Round [67] log likelihood: -31480.927654
EM: Round [68] log likelihood: -31480.925716
EM: Round [69] log likelihood: -31480.923779
EM: Round [70] log likelihood: -31480.921846
EM: Round [71] log likelihood: -31480.919914
EM: Round [72] log likelihood: -31480.917985
EM: Round [73] log likelihood: -31480.916058
EM: Round [74] log likelihood: -31480.914134
EM: Round [75] log likelihood: -31480.912212
EM: Round [76] log likelihood: -31480.910292
EM: Round [77] log likelihood: -31480.908375
EM: Round [78] log likelihood: -31480.906460
EM: Round [79] log likelihood: -31480.904547
EM: Round [80] log likelihood: -31480.902637
EM: Round [81] log likelihood: -31480.900729
EM: Round [82] log likelihood: -31480.898823
EM: Round [83] log likelihood: -31480.896920
EM: Round [84] log likelihood: -31480.895019
EM: Round [85] log likelihood: -31480.893120
EM: Round [86] log likelihood: -31480.891224
EM: Round [87] log likelihood: -31480.889330
EM: Round [88] log likelihood: -31480.887438
EM: Round [89] log likelihood: -31480.885548
EM: Round [90] log likelihood: -31480.883661
EM: Round [91] log likelihood: -31480.881776
EM: Round [92] log likelihood: -31480.879893
EM: Round [93] log likelihood: -31480.878013
EM: Round [94] log likelihood: -31480.876135
EM: Round [95] log likelihood: -31480.874259
EM: Round [96] log likelihood: -31480.872385
EM: Round [97] log likelihood: -31480.870514
EM: Round [98] log likelihood: -31480.868645
EM: Round [99] log likelihood: -31480.866778
EM: Round [100] log likelihood: -31480.864913
EM: Round [101] log likelihood: -31480.863051
EM: Round [102] log likelihood: -31480.861190
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EM: Round [565] log likelihood: -31480.181000
EM: Round [566] log likelihood: -31480.179830
EM: Round [567] log likelihood: -31480.178660
EM: Round [568] log likelihood: -31480.177492
EM: Round [569] log likelihood: -31480.176325
EM: Round [570] log likelihood: -31480.175159
EM: Round [571] log likelihood: -31480.173994
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EM: Round [579] log likelihood: -31480.164707
EM: Round [580] log likelihood: -31480.163551
EM: Round [581] log likelihood: -31480.162396
EM: Round [582] log likelihood: -31480.161241
EM: Round [583] log likelihood: -31480.160088
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EM: Round [598] log likelihood: -31480.142902
EM: Round [599] log likelihood: -31480.141763
EM: Round [600] log likelihood: -31480.140626
EM: Round [601] log likelihood: -31480.139490
EM: Round [602] log likelihood: -31480.138355
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EM: Round [605] log likelihood: -31480.134955
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EM: Round [610] log likelihood: -31480.129307
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EM: Round [616] log likelihood: -31480.122560
EM: Round [617] log likelihood: -31480.121438
EM: Round [618] log likelihood: -31480.120318
EM: Round [619] log likelihood: -31480.119199
EM: Round [620] log likelihood: -31480.118080
EM: Round [621] log likelihood: -31480.116963
EM: Round [622] log likelihood: -31480.115846
EM: Round [623] log likelihood: -31480.114730
EM: Round [624] log likelihood: -31480.113615
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EM: Round [632] log likelihood: -31480.104730
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EM: Round [956] log likelihood: -31479.787521
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EM: Round [974] log likelihood: -31479.772011
EM: Round [975] log likelihood: -31479.771155
EM: Round [976] log likelihood: -31479.770299
EM: Round [977] log likelihood: -31479.769444
EM: Round [978] log likelihood: -31479.768590
EM: Round [979] log likelihood: -31479.767736
EM: Round [980] log likelihood: -31479.766883
EM: Round [981] log likelihood: -31479.766031
EM: Round [982] log likelihood: -31479.765179
EM: Round [983] log likelihood: -31479.764328
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EM: Round [985] log likelihood: -31479.762627
EM: Round [986] log likelihood: -31479.761777
EM: Round [987] log likelihood: -31479.760928
EM: Round [988] log likelihood: -31479.760080
EM: Round [989] log likelihood: -31479.759232
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EM: Round [992] log likelihood: -31479.756692
EM: Round [993] log likelihood: -31479.755847
EM: Round [994] log likelihood: -31479.755002
EM: Round [995] log likelihood: -31479.754158
EM: Round [996] log likelihood: -31479.753314
EM: Round [997] log likelihood: -31479.752471
EM: Round [998] log likelihood: -31479.751628
EM: Round [999] log likelihood: -31479.750786
EM: Round [1000] log likelihood: -31479.749945
EM: Round [1001] log likelihood: -31479.749104
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.02 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam into /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.read_coords > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa > /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -27915.700733
EM: Round [1] log likelihood: -27915.387910
EM: Round [2] log likelihood: -27915.384568
EM: Round [3] log likelihood: -27915.382967
EM: Round [4] log likelihood: -27915.381387
EM: Round [5] log likelihood: -27915.379809
EM: Round [6] log likelihood: -27915.378233
EM: Round [7] log likelihood: -27915.376659
EM: Round [8] log likelihood: -27915.375086
EM: Round [9] log likelihood: -27915.373515
EM: Round [10] log likelihood: -27915.371946
EM: Round [11] log likelihood: -27915.370378
EM: Round [12] log likelihood: -27915.368812
EM: Round [13] log likelihood: -27915.367247
EM: Round [14] log likelihood: -27915.365684
EM: Round [15] log likelihood: -27915.364123
EM: Round [16] log likelihood: -27915.362564
EM: Round [17] log likelihood: -27915.361006
EM: Round [18] log likelihood: -27915.359449
EM: Round [19] log likelihood: -27915.357894
EM: Round [20] log likelihood: -27915.356341
EM: Round [21] log likelihood: -27915.354790
EM: Round [22] log likelihood: -27915.353240
EM: Round [23] log likelihood: -27915.351692
EM: Round [24] log likelihood: -27915.350145
EM: Round [25] log likelihood: -27915.348600
EM: Round [26] log likelihood: -27915.347057
EM: Round [27] log likelihood: -27915.345515
EM: Round [28] log likelihood: -27915.343974
EM: Round [29] log likelihood: -27915.342436
EM: Round [30] log likelihood: -27915.340899
EM: Round [31] log likelihood: -27915.339363
EM: Round [32] log likelihood: -27915.337829
EM: Round [33] log likelihood: -27915.336297
EM: Round [34] log likelihood: -27915.334766
EM: Round [35] log likelihood: -27915.333237
EM: Round [36] log likelihood: -27915.331709
EM: Round [37] log likelihood: -27915.330183
EM: Round [38] log likelihood: -27915.328659
EM: Round [39] log likelihood: -27915.327136
EM: Round [40] log likelihood: -27915.325615
EM: Round [41] log likelihood: -27915.324095
EM: Round [42] log likelihood: -27915.322577
EM: Round [43] log likelihood: -27915.321060
EM: Round [44] log likelihood: -27915.319545
EM: Round [45] log likelihood: -27915.318031
EM: Round [46] log likelihood: -27915.316519
EM: Round [47] log likelihood: -27915.315009
EM: Round [48] log likelihood: -27915.313500
EM: Round [49] log likelihood: -27915.311992
EM: Round [50] log likelihood: -27915.310486
EM: Round [51] log likelihood: -27915.308982
EM: Round [52] log likelihood: -27915.307479
EM: Round [53] log likelihood: -27915.305978
EM: Round [54] log likelihood: -27915.304478
EM: Round [55] log likelihood: -27915.302980
EM: Round [56] log likelihood: -27915.301483
EM: Round [57] log likelihood: -27915.299988
EM: Round [58] log likelihood: -27915.298494
EM: Round [59] log likelihood: -27915.297002
EM: Round [60] log likelihood: -27915.295511
EM: Round [61] log likelihood: -27915.294022
EM: Round [62] log likelihood: -27915.292534
EM: Round [63] log likelihood: -27915.291048
EM: Round [64] log likelihood: -27915.289563
EM: Round [65] log likelihood: -27915.288080
EM: Round [66] log likelihood: -27915.286598
EM: Round [67] log likelihood: -27915.285118
EM: Round [68] log likelihood: -27915.283639
EM: Round [69] log likelihood: -27915.282162
EM: Round [70] log likelihood: -27915.280686
EM: Round [71] log likelihood: -27915.279212
EM: Round [72] log likelihood: -27915.277739
EM: Round [73] log likelihood: -27915.276268
EM: Round [74] log likelihood: -27915.274798
EM: Round [75] log likelihood: -27915.273330
EM: Round [76] log likelihood: -27915.271863
EM: Round [77] log likelihood: -27915.270397
EM: Round [78] log likelihood: -27915.268933
EM: Round [79] log likelihood: -27915.267471
EM: Round [80] log likelihood: -27915.266010
EM: Round [81] log likelihood: -27915.264550
EM: Round [82] log likelihood: -27915.263092
EM: Round [83] log likelihood: -27915.261635
EM: Round [84] log likelihood: -27915.260180
EM: Round [85] log likelihood: -27915.258726
EM: Round [86] log likelihood: -27915.257273
EM: Round [87] log likelihood: -27915.255822
EM: Round [88] log likelihood: -27915.254373
EM: Round [89] log likelihood: -27915.252925
EM: Round [90] log likelihood: -27915.251478
EM: Round [91] log likelihood: -27915.250033
EM: Round [92] log likelihood: -27915.248589
EM: Round [93] log likelihood: -27915.247146
EM: Round [94] log likelihood: -27915.245705
EM: Round [95] log likelihood: -27915.244266
EM: Round [96] log likelihood: -27915.242828
EM: Round [97] log likelihood: -27915.241391
EM: Round [98] log likelihood: -27915.239955
EM: Round [99] log likelihood: -27915.238522
EM: Round [100] log likelihood: -27915.237089
EM: Round [101] log likelihood: -27915.235658
EM: Round [102] log likelihood: -27915.234228
EM: Round [103] log likelihood: -27915.232800
EM: Round [104] log likelihood: -27915.231373
EM: Round [105] log likelihood: -27915.229947
EM: Round [106] log likelihood: -27915.228523
EM: Round [107] log likelihood: -27915.227100
EM: Round [108] log likelihood: -27915.225679
EM: Round [109] log likelihood: -27915.224259
EM: Round [110] log likelihood: -27915.222840
EM: Round [111] log likelihood: -27915.221423
EM: Round [112] log likelihood: -27915.220007
EM: Round [113] log likelihood: -27915.218593
EM: Round [114] log likelihood: -27915.217180
EM: Round [115] log likelihood: -27915.215768
EM: Round [116] log likelihood: -27915.214358
EM: Round [117] log likelihood: -27915.212949
EM: Round [118] log likelihood: -27915.211541
EM: Round [119] log likelihood: -27915.210135
EM: Round [120] log likelihood: -27915.208730
EM: Round [121] log likelihood: -27915.207326
EM: Round [122] log likelihood: -27915.205924
EM: Round [123] log likelihood: -27915.204523
EM: Round [124] log likelihood: -27915.203124
EM: Round [125] log likelihood: -27915.201726
EM: Round [126] log likelihood: -27915.200329
EM: Round [127] log likelihood: -27915.198934
EM: Round [128] log likelihood: -27915.197539
EM: Round [129] log likelihood: -27915.196147
EM: Round [130] log likelihood: -27915.194755
EM: Round [131] log likelihood: -27915.193365
EM: Round [132] log likelihood: -27915.191976
EM: Round [133] log likelihood: -27915.190589
EM: Round [134] log likelihood: -27915.189203
EM: Round [135] log likelihood: -27915.187818
EM: Round [136] log likelihood: -27915.186435
EM: Round [137] log likelihood: -27915.185053
EM: Round [138] log likelihood: -27915.183672
EM: Round [139] log likelihood: -27915.182292
EM: Round [140] log likelihood: -27915.180914
EM: Round [141] log likelihood: -27915.179537
EM: Round [142] log likelihood: -27915.178162
EM: Round [143] log likelihood: -27915.176787
EM: Round [144] log likelihood: -27915.175414
EM: Round [145] log likelihood: -27915.174043
EM: Round [146] log likelihood: -27915.172672
EM: Round [147] log likelihood: -27915.171303
EM: Round [148] log likelihood: -27915.169936
EM: Round [149] log likelihood: -27915.168569
EM: Round [150] log likelihood: -27915.167204
EM: Round [151] log likelihood: -27915.165840
EM: Round [152] log likelihood: -27915.164478
EM: Round [153] log likelihood: -27915.163116
EM: Round [154] log likelihood: -27915.161756
EM: Round [155] log likelihood: -27915.160398
EM: Round [156] log likelihood: -27915.159040
EM: Round [157] log likelihood: -27915.157684
EM: Round [158] log likelihood: -27915.156329
EM: Round [159] log likelihood: -27915.154976
EM: Round [160] log likelihood: -27915.153623
EM: Round [161] log likelihood: -27915.152272
EM: Round [162] log likelihood: -27915.150923
EM: Round [163] log likelihood: -27915.149574
EM: Round [164] log likelihood: -27915.148227
EM: Round [165] log likelihood: -27915.146881
EM: Round [166] log likelihood: -27915.145536
EM: Round [167] log likelihood: -27915.144193
EM: Round [168] log likelihood: -27915.142850
EM: Round [169] log likelihood: -27915.141509
EM: Round [170] log likelihood: -27915.140170
EM: Round [171] log likelihood: -27915.138831
EM: Round [172] log likelihood: -27915.137494
EM: Round [173] log likelihood: -27915.136158
EM: Round [174] log likelihood: -27915.134823
EM: Round [175] log likelihood: -27915.133490
EM: Round [176] log likelihood: -27915.132158
EM: Round [177] log likelihood: -27915.130827
EM: Round [178] log likelihood: -27915.129497
EM: Round [179] log likelihood: -27915.128168
EM: Round [180] log likelihood: -27915.126841
EM: Round [181] log likelihood: -27915.125515
EM: Round [182] log likelihood: -27915.124190
EM: Round [183] log likelihood: -27915.122867
EM: Round [184] log likelihood: -27915.121544
EM: Round [185] log likelihood: -27915.120223
EM: Round [186] log likelihood: -27915.118903
EM: Round [187] log likelihood: -27915.117585
EM: Round [188] log likelihood: -27915.116267
EM: Round [189] log likelihood: -27915.114951
EM: Round [190] log likelihood: -27915.113636
EM: Round [191] log likelihood: -27915.112322
EM: Round [192] log likelihood: -27915.111009
EM: Round [193] log likelihood: -27915.109698
EM: Round [194] log likelihood: -27915.108388
EM: Round [195] log likelihood: -27915.107079
EM: Round [196] log likelihood: -27915.105771
EM: Round [197] log likelihood: -27915.104464
EM: Round [198] log likelihood: -27915.103159
EM: Round [199] log likelihood: -27915.101854
EM: Round [200] log likelihood: -27915.100551
EM: Round [201] log likelihood: -27915.099250
EM: Round [202] log likelihood: -27915.097949
EM: Round [203] log likelihood: -27915.096650
EM: Round [204] log likelihood: -27915.095351
EM: Round [205] log likelihood: -27915.094054
EM: Round [206] log likelihood: -27915.092758
EM: Round [207] log likelihood: -27915.091464
EM: Round [208] log likelihood: -27915.090170
EM: Round [209] log likelihood: -27915.088878
EM: Round [210] log likelihood: -27915.087586
EM: Round [211] log likelihood: -27915.086296
EM: Round [212] log likelihood: -27915.085008
EM: Round [213] log likelihood: -27915.083720
EM: Round [214] log likelihood: -27915.082433
EM: Round [215] log likelihood: -27915.081148
EM: Round [216] log likelihood: -27915.079864
EM: Round [217] log likelihood: -27915.078581
EM: Round [218] log likelihood: -27915.077299
EM: Round [219] log likelihood: -27915.076018
EM: Round [220] log likelihood: -27915.074739
EM: Round [221] log likelihood: -27915.073460
EM: Round [222] log likelihood: -27915.072183
EM: Round [223] log likelihood: -27915.070907
EM: Round [224] log likelihood: -27915.069632
EM: Round [225] log likelihood: -27915.068358
EM: Round [226] log likelihood: -27915.067086
EM: Round [227] log likelihood: -27915.065814
EM: Round [228] log likelihood: -27915.064544
EM: Round [229] log likelihood: -27915.063275
EM: Round [230] log likelihood: -27915.062007
EM: Round [231] log likelihood: -27915.060740
EM: Round [232] log likelihood: -27915.059474
EM: Round [233] log likelihood: -27915.058209
EM: Round [234] log likelihood: -27915.056946
EM: Round [235] log likelihood: -27915.055684
EM: Round [236] log likelihood: -27915.054422
EM: Round [237] log likelihood: -27915.053162
EM: Round [238] log likelihood: -27915.051903
EM: Round [239] log likelihood: -27915.050645
EM: Round [240] log likelihood: -27915.049389
EM: Round [241] log likelihood: -27915.048133
EM: Round [242] log likelihood: -27915.046879
EM: Round [243] log likelihood: -27915.045625
EM: Round [244] log likelihood: -27915.044373
EM: Round [245] log likelihood: -27915.043122
EM: Round [246] log likelihood: -27915.041872
EM: Round [247] log likelihood: -27915.040623
EM: Round [248] log likelihood: -27915.039375
EM: Round [249] log likelihood: -27915.038128
EM: Round [250] log likelihood: -27915.036883
EM: Round [251] log likelihood: -27915.035638
EM: Round [252] log likelihood: -27915.034395
EM: Round [253] log likelihood: -27915.033152
EM: Round [254] log likelihood: -27915.031911
EM: Round [255] log likelihood: -27915.030671
EM: Round [256] log likelihood: -27915.029432
EM: Round [257] log likelihood: -27915.028194
EM: Round [258] log likelihood: -27915.026957
EM: Round [259] log likelihood: -27915.025722
EM: Round [260] log likelihood: -27915.024487
EM: Round [261] log likelihood: -27915.023254
EM: Round [262] log likelihood: -27915.022021
EM: Round [263] log likelihood: -27915.020790
EM: Round [264] log likelihood: -27915.019559
EM: Round [265] log likelihood: -27915.018330
EM: Round [266] log likelihood: -27915.017102
EM: Round [267] log likelihood: -27915.015875
EM: Round [268] log likelihood: -27915.014649
EM: Round [269] log likelihood: -27915.013424
EM: Round [270] log likelihood: -27915.012200
EM: Round [271] log likelihood: -27915.010978
EM: Round [272] log likelihood: -27915.009756
EM: Round [273] log likelihood: -27915.008535
EM: Round [274] log likelihood: -27915.007316
EM: Round [275] log likelihood: -27915.006097
EM: Round [276] log likelihood: -27915.004880
EM: Round [277] log likelihood: -27915.003663
EM: Round [278] log likelihood: -27915.002448
EM: Round [279] log likelihood: -27915.001234
EM: Round [280] log likelihood: -27915.000021
EM: Round [281] log likelihood: -27914.998809
EM: Round [282] log likelihood: -27914.997597
EM: Round [283] log likelihood: -27914.996387
EM: Round [284] log likelihood: -27914.995178
EM: Round [285] log likelihood: -27914.993971
EM: Round [286] log likelihood: -27914.992764
EM: Round [287] log likelihood: -27914.991558
EM: Round [288] log likelihood: -27914.990353
EM: Round [289] log likelihood: -27914.989149
EM: Round [290] log likelihood: -27914.987947
EM: Round [291] log likelihood: -27914.986745
EM: Round [292] log likelihood: -27914.985544
EM: Round [293] log likelihood: -27914.984345
EM: Round [294] log likelihood: -27914.983146
EM: Round [295] log likelihood: -27914.981949
EM: Round [296] log likelihood: -27914.980752
EM: Round [297] log likelihood: -27914.979557
EM: Round [298] log likelihood: -27914.978362
EM: Round [299] log likelihood: -27914.977169
EM: Round [300] log likelihood: -27914.975977
EM: Round [301] log likelihood: -27914.974785
EM: Round [302] log likelihood: -27914.973595
EM: Round [303] log likelihood: -27914.972406
EM: Round [304] log likelihood: -27914.971218
EM: Round [305] log likelihood: -27914.970030
EM: Round [306] log likelihood: -27914.968844
EM: Round [307] log likelihood: -27914.967659
EM: Round [308] log likelihood: -27914.966475
EM: Round [309] log likelihood: -27914.965291
EM: Round [310] log likelihood: -27914.964109
EM: Round [311] log likelihood: -27914.962928
EM: Round [312] log likelihood: -27914.961748
EM: Round [313] log likelihood: -27914.960569
EM: Round [314] log likelihood: -27914.959391
EM: Round [315] log likelihood: -27914.958214
EM: Round [316] log likelihood: -27914.957037
EM: Round [317] log likelihood: -27914.955862
EM: Round [318] log likelihood: -27914.954688
EM: Round [319] log likelihood: -27914.953515
EM: Round [320] log likelihood: -27914.952343
EM: Round [321] log likelihood: -27914.951172
EM: Round [322] log likelihood: -27914.950002
EM: Round [323] log likelihood: -27914.948833
EM: Round [324] log likelihood: -27914.947664
EM: Round [325] log likelihood: -27914.946497
EM: Round [326] log likelihood: -27914.945331
EM: Round [327] log likelihood: -27914.944166
EM: Round [328] log likelihood: -27914.943002
EM: Round [329] log likelihood: -27914.941838
EM: Round [330] log likelihood: -27914.940676
EM: Round [331] log likelihood: -27914.939515
EM: Round [332] log likelihood: -27914.938355
EM: Round [333] log likelihood: -27914.937195
EM: Round [334] log likelihood: -27914.936037
EM: Round [335] log likelihood: -27914.934880
EM: Round [336] log likelihood: -27914.933723
EM: Round [337] log likelihood: -27914.932568
EM: Round [338] log likelihood: -27914.931414
EM: Round [339] log likelihood: -27914.930260
EM: Round [340] log likelihood: -27914.929108
EM: Round [341] log likelihood: -27914.927956
EM: Round [342] log likelihood: -27914.926806
EM: Round [343] log likelihood: -27914.925656
EM: Round [344] log likelihood: -27914.924508
EM: Round [345] log likelihood: -27914.923360
EM: Round [346] log likelihood: -27914.922213
EM: Round [347] log likelihood: -27914.921068
EM: Round [348] log likelihood: -27914.919923
EM: Round [349] log likelihood: -27914.918779
EM: Round [350] log likelihood: -27914.917636
EM: Round [351] log likelihood: -27914.916494
EM: Round [352] log likelihood: -27914.915353
EM: Round [353] log likelihood: -27914.914213
EM: Round [354] log likelihood: -27914.913074
EM: Round [355] log likelihood: -27914.911936
EM: Round [356] log likelihood: -27914.910799
EM: Round [357] log likelihood: -27914.909663
EM: Round [358] log likelihood: -27914.908528
EM: Round [359] log likelihood: -27914.907393
EM: Round [360] log likelihood: -27914.906260
EM: Round [361] log likelihood: -27914.905127
EM: Round [362] log likelihood: -27914.903996
EM: Round [363] log likelihood: -27914.902865
EM: Round [364] log likelihood: -27914.901736
EM: Round [365] log likelihood: -27914.900607
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EM: Round [824] log likelihood: -27914.464227
EM: Round [825] log likelihood: -27914.463424
EM: Round [826] log likelihood: -27914.462622
EM: Round [827] log likelihood: -27914.461820
EM: Round [828] log likelihood: -27914.461018
EM: Round [829] log likelihood: -27914.460217
EM: Round [830] log likelihood: -27914.459417
EM: Round [831] log likelihood: -27914.458617
EM: Round [832] log likelihood: -27914.457818
EM: Round [833] log likelihood: -27914.457019
EM: Round [834] log likelihood: -27914.456221
EM: Round [835] log likelihood: -27914.455423
EM: Round [836] log likelihood: -27914.454626
EM: Round [837] log likelihood: -27914.453829
EM: Round [838] log likelihood: -27914.453033
EM: Round [839] log likelihood: -27914.452237
EM: Round [840] log likelihood: -27914.451442
EM: Round [841] log likelihood: -27914.450647
EM: Round [842] log likelihood: -27914.449853
EM: Round [843] log likelihood: -27914.449060
EM: Round [844] log likelihood: -27914.448267
EM: Round [845] log likelihood: -27914.447474
EM: Round [846] log likelihood: -27914.446682
EM: Round [847] log likelihood: -27914.445891
EM: Round [848] log likelihood: -27914.445100
EM: Round [849] log likelihood: -27914.444309
EM: Round [850] log likelihood: -27914.443520
EM: Round [851] log likelihood: -27914.442730
EM: Round [852] log likelihood: -27914.441941
EM: Round [853] log likelihood: -27914.441153
EM: Round [854] log likelihood: -27914.440365
EM: Round [855] log likelihood: -27914.439578
EM: Round [856] log likelihood: -27914.438791
EM: Round [857] log likelihood: -27914.438005
EM: Round [858] log likelihood: -27914.437219
EM: Round [859] log likelihood: -27914.436434
EM: Round [860] log likelihood: -27914.435649
EM: Round [861] log likelihood: -27914.434865
EM: Round [862] log likelihood: -27914.434081
EM: Round [863] log likelihood: -27914.433298
EM: Round [864] log likelihood: -27914.432516
EM: Round [865] log likelihood: -27914.431733
EM: Round [866] log likelihood: -27914.430952
EM: Round [867] log likelihood: -27914.430171
EM: Round [868] log likelihood: -27914.429390
EM: Round [869] log likelihood: -27914.428610
EM: Round [870] log likelihood: -27914.427830
EM: Round [871] log likelihood: -27914.427051
EM: Round [872] log likelihood: -27914.426273
EM: Round [873] log likelihood: -27914.425495
EM: Round [874] log likelihood: -27914.424717
EM: Round [875] log likelihood: -27914.423940
EM: Round [876] log likelihood: -27914.423164
EM: Round [877] log likelihood: -27914.422388
EM: Round [878] log likelihood: -27914.421612
EM: Round [879] log likelihood: -27914.420837
EM: Round [880] log likelihood: -27914.420063
EM: Round [881] log likelihood: -27914.419289
EM: Round [882] log likelihood: -27914.418515
EM: Round [883] log likelihood: -27914.417742
EM: Round [884] log likelihood: -27914.416970
EM: Round [885] log likelihood: -27914.416198
EM: Round [886] log likelihood: -27914.415426
EM: Round [887] log likelihood: -27914.414655
EM: Round [888] log likelihood: -27914.413885
EM: Round [889] log likelihood: -27914.413115
EM: Round [890] log likelihood: -27914.412345
EM: Round [891] log likelihood: -27914.411576
EM: Round [892] log likelihood: -27914.410808
EM: Round [893] log likelihood: -27914.410040
EM: Round [894] log likelihood: -27914.409272
EM: Round [895] log likelihood: -27914.408505
EM: Round [896] log likelihood: -27914.407739
EM: Round [897] log likelihood: -27914.406973
EM: Round [898] log likelihood: -27914.406207
EM: Round [899] log likelihood: -27914.405442
EM: Round [900] log likelihood: -27914.404678
EM: Round [901] log likelihood: -27914.403914
EM: Round [902] log likelihood: -27914.403150
EM: Round [903] log likelihood: -27914.402387
EM: Round [904] log likelihood: -27914.401625
EM: Round [905] log likelihood: -27914.400862
EM: Round [906] log likelihood: -27914.400101
EM: Round [907] log likelihood: -27914.399340
EM: Round [908] log likelihood: -27914.398579
EM: Round [909] log likelihood: -27914.397819
EM: Round [910] log likelihood: -27914.397060
EM: Round [911] log likelihood: -27914.396300
EM: Round [912] log likelihood: -27914.395542
EM: Round [913] log likelihood: -27914.394784
EM: Round [914] log likelihood: -27914.394026
EM: Round [915] log likelihood: -27914.393269
EM: Round [916] log likelihood: -27914.392512
EM: Round [917] log likelihood: -27914.391756
EM: Round [918] log likelihood: -27914.391000
EM: Round [919] log likelihood: -27914.390245
EM: Round [920] log likelihood: -27914.389490
EM: Round [921] log likelihood: -27914.388736
EM: Round [922] log likelihood: -27914.387982
EM: Round [923] log likelihood: -27914.387229
EM: Round [924] log likelihood: -27914.386476
EM: Round [925] log likelihood: -27914.385724
EM: Round [926] log likelihood: -27914.384972
EM: Round [927] log likelihood: -27914.384221
EM: Round [928] log likelihood: -27914.383470
EM: Round [929] log likelihood: -27914.382720
EM: Round [930] log likelihood: -27914.381970
EM: Round [931] log likelihood: -27914.381220
EM: Round [932] log likelihood: -27914.380471
EM: Round [933] log likelihood: -27914.379723
EM: Round [934] log likelihood: -27914.378975
EM: Round [935] log likelihood: -27914.378227
EM: Round [936] log likelihood: -27914.377480
EM: Round [937] log likelihood: -27914.376734
EM: Round [938] log likelihood: -27914.375988
EM: Round [939] log likelihood: -27914.375242
EM: Round [940] log likelihood: -27914.374497
EM: Round [941] log likelihood: -27914.373752
EM: Round [942] log likelihood: -27914.373008
EM: Round [943] log likelihood: -27914.372264
EM: Round [944] log likelihood: -27914.371521
EM: Round [945] log likelihood: -27914.370778
EM: Round [946] log likelihood: -27914.370036
EM: Round [947] log likelihood: -27914.369294
EM: Round [948] log likelihood: -27914.368553
EM: Round [949] log likelihood: -27914.367812
EM: Round [950] log likelihood: -27914.367072
EM: Round [951] log likelihood: -27914.366332
EM: Round [952] log likelihood: -27914.365592
EM: Round [953] log likelihood: -27914.364853
EM: Round [954] log likelihood: -27914.364115
EM: Round [955] log likelihood: -27914.363377
EM: Round [956] log likelihood: -27914.362639
EM: Round [957] log likelihood: -27914.361902
EM: Round [958] log likelihood: -27914.361165
EM: Round [959] log likelihood: -27914.360429
EM: Round [960] log likelihood: -27914.359693
EM: Round [961] log likelihood: -27914.358958
EM: Round [962] log likelihood: -27914.358223
EM: Round [963] log likelihood: -27914.357489
EM: Round [964] log likelihood: -27914.356755
EM: Round [965] log likelihood: -27914.356021
EM: Round [966] log likelihood: -27914.355289
EM: Round [967] log likelihood: -27914.354556
EM: Round [968] log likelihood: -27914.353824
EM: Round [969] log likelihood: -27914.353092
EM: Round [970] log likelihood: -27914.352361
EM: Round [971] log likelihood: -27914.351631
EM: Round [972] log likelihood: -27914.350901
EM: Round [973] log likelihood: -27914.350171
EM: Round [974] log likelihood: -27914.349442
EM: Round [975] log likelihood: -27914.348713
EM: Round [976] log likelihood: -27914.347984
EM: Round [977] log likelihood: -27914.347256
EM: Round [978] log likelihood: -27914.346529
EM: Round [979] log likelihood: -27914.345802
EM: Round [980] log likelihood: -27914.345076
EM: Round [981] log likelihood: -27914.344349
EM: Round [982] log likelihood: -27914.343624
EM: Round [983] log likelihood: -27914.342899
EM: Round [984] log likelihood: -27914.342174
EM: Round [985] log likelihood: -27914.341450
EM: Round [986] log likelihood: -27914.340726
EM: Round [987] log likelihood: -27914.340003
EM: Round [988] log likelihood: -27914.339280
EM: Round [989] log likelihood: -27914.338557
EM: Round [990] log likelihood: -27914.337835
EM: Round [991] log likelihood: -27914.337114
EM: Round [992] log likelihood: -27914.336393
EM: Round [993] log likelihood: -27914.335672
EM: Round [994] log likelihood: -27914.334952
EM: Round [995] log likelihood: -27914.334232
EM: Round [996] log likelihood: -27914.333513
EM: Round [997] log likelihood: -27914.332794
EM: Round [998] log likelihood: -27914.332076
EM: Round [999] log likelihood: -27914.331358
EM: Round [1000] log likelihood: -27914.330640
EM: Round [1001] log likelihood: -27914.329923
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz: 288891863
Execution Time = 5.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa --gtf /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fa --gtf /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gtf > /tmp/nxf.Q3SoObmB84/fi_workdir/microH.dat
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Q3SoObmB84/fi_workdir/microH.dat /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.Q3SoObmB84/fi_workdir/microH.dat /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Q3SoObmB84 --json_outfile /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Q3SoObmB84 --json_outfile /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1
Running: touch /tmp/nxf.Q3SoObmB84/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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1 --html_output /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 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.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1 --html_output /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000228526.7]
WARNING, no entry stored in dbm for [ENSG00000228526.7]
WARNING, no entry stored in dbm for [ENSG00000228735.1]
WARNING, no entry stored in dbm for [ENSG00000078319.10]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000078319.10]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000078319.10]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000078319.10]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
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 [ENSG00000223698.3]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Q3SoObmB84/ctat_genome_lib_build_dir > /tmp/nxf.Q3SoObmB84/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.Q3SoObmB84/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory