Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/f37a9b33c130d908f67d3151b5ac52/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.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/79/f37a9b33c130d908f67d3151b5ac52/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e5f90ccb6505bf5501e38c35f8bc98/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/da58afd6710759c103e6fa6d38193c/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e5f90ccb6505bf5501e38c35f8bc98/.command.run
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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 BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/cytoBand.txt
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed
-parsing GTF file: /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.wrwpEnYaAa/fi_workdir --reads "/tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:27:52 ..... started STAR run
Jun 08 10:27:52 ..... loading genome
Jun 08 10:29:35 ... generating Suffix Array index
Jun 08 10:33:25 ... completed Suffix Array index
Jun 08 10:33:26 ..... processing annotations GTF
Jun 08 10:33:26 ..... inserting junctions into the genome indices
Jun 08 10:34:27 ..... started mapping
Jun 08 11:53:38 ..... finished mapping
Jun 08 11:53:39 ..... started sorting BAM
Jun 08 11:53:40 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam
Execution Time = 85.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.wrwpEnYaAa/fi_workdir --reads "/tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:53:57 : INFO : Done.
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
-parsing /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
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[2790000] -done parsing /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 295,
'seq-similar region overlap' => 9,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 203,
' ** passed ** ' => 4986,
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 16,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 32,
'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 38,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 78,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 102,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 16,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 606,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 364,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 18,
'excessive soft clipping' => 19841,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 1698,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 214,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 162,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 471,
'num_hits: 10 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 7 != num_counted_on_fusion_contigs 2 ' => 4,
'small anchor length' => 21,
'num genes matched < 2' => 28,
'per_id < 96' => 14114,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 8,
'num_hits: 9 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 19,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 152,
'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 28,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 48,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 26,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 33,
'low complexity anchor region' => 20,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 33,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 2063,
'exons hit < 2' => 7,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 27
};
-writing fusion junction support info.
Execution Time = 1.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[488000] -fusion SPANNING read extraction for scaff: PDXDC2P--NPIPB3
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[101000] -fusion SPANNING read extraction for scaff: PIEZO2--KCNIP4
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[98000] -fusion SPANNING read extraction for scaff: PIEZO2--AC096719.1
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[95000] -fusion SPANNING read extraction for scaff: PIEZO2--SLC35F1
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[190000] -fusion SPANNING read extraction for scaff: RAB11FIP1--TRAPPC9
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[56000] -fusion SPANNING read extraction for scaff: RMND1--AC090578.1
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[91000] -fusion SPANNING read extraction for scaff: SLC20A2--TRAPPC9
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[10000] -fusion SPANNING read extraction for scaff: STAM--AC069545.1
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[31000] -fusion SPANNING read extraction for scaff: STAM--ZWINT
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[94000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[31000]
[32000]
[33000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000] -fusion SPANNING read extraction for scaff: TOGARAM1--NUBPL
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000] -fusion SPANNING read extraction for scaff: XPNPEP1--AL590623.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000] -fusion SPANNING read extraction for scaff: XPNPEP1--KSR1P1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 2122,
'lacks exon overlap' => 79255
};
Execution Time = 4.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -8256.392321
EM: Round [1] log likelihood: -8249.837459
EM: Round [2] log likelihood: -8247.937959
EM: Round [3] log likelihood: -8247.140481
EM: Round [4] log likelihood: -8246.768654
EM: Round [5] log likelihood: -8246.571795
EM: Round [6] log likelihood: -8246.452763
EM: Round [7] log likelihood: -8246.372258
EM: Round [8] log likelihood: -8246.313364
EM: Round [9] log likelihood: -8246.268101
EM: Round [10] log likelihood: -8246.232238
EM: Round [11] log likelihood: -8246.203243
EM: Round [12] log likelihood: -8246.179442
EM: Round [13] log likelihood: -8246.159653
EM: Round [14] log likelihood: -8246.143005
EM: Round [15] log likelihood: -8246.128842
EM: Round [16] log likelihood: -8246.116664
EM: Round [17] log likelihood: -8246.106088
EM: Round [18] log likelihood: -8246.096814
EM: Round [19] log likelihood: -8246.088613
EM: Round [20] log likelihood: -8246.081303
EM: Round [21] log likelihood: -8246.074744
EM: Round [22] log likelihood: -8246.068822
EM: Round [23] log likelihood: -8246.063447
EM: Round [24] log likelihood: -8246.058547
EM: Round [25] log likelihood: -8246.054064
EM: Round [26] log likelihood: -8246.049949
EM: Round [27] log likelihood: -8246.046161
EM: Round [28] log likelihood: -8246.042668
EM: Round [29] log likelihood: -8246.039439
EM: Round [30] log likelihood: -8246.036451
EM: Round [31] log likelihood: -8246.033682
EM: Round [32] log likelihood: -8246.031114
EM: Round [33] log likelihood: -8246.028729
EM: Round [34] log likelihood: -8246.026513
EM: Round [35] log likelihood: -8246.024453
EM: Round [36] log likelihood: -8246.022537
EM: Round [37] log likelihood: -8246.020754
EM: Round [38] log likelihood: -8246.019094
EM: Round [39] log likelihood: -8246.017549
EM: Round [40] log likelihood: -8246.016109
EM: Round [41] log likelihood: -8246.014768
EM: Round [42] log likelihood: -8246.013518
EM: Round [43] log likelihood: -8246.012354
EM: Round [44] log likelihood: -8246.011269
EM: Round [45] log likelihood: -8246.010257
EM: Round [46] log likelihood: -8246.009313
EM: Round [47] log likelihood: -8246.008434
EM: Round [48] log likelihood: -8246.007614
EM: Round [49] log likelihood: -8246.006849
EM: Round [50] log likelihood: -8246.006136
EM: Round [51] log likelihood: -8246.005471
EM: Round [52] log likelihood: -8246.004851
EM: Round [53] log likelihood: -8246.004272
EM: Round [54] log likelihood: -8246.003732
EM: Round [55] log likelihood: -8246.003229
EM: Round [56] log likelihood: -8246.002759
EM: Round [57] log likelihood: -8246.002321
EM: Round [58] log likelihood: -8246.001912
EM: Round [59] log likelihood: -8246.001531
EM: Round [60] log likelihood: -8246.001175
EM: Round [61] log likelihood: -8246.000843
EM: Round [62] log likelihood: -8246.000533
EM: Round [63] log likelihood: -8246.000244
EM: Round [64] log likelihood: -8245.999974
EM: Round [65] log likelihood: -8245.999723
EM: Round [66] log likelihood: -8245.999488
EM: Round [67] log likelihood: -8245.999269
EM: Round [68] log likelihood: -8245.999064
EM: Round [69] log likelihood: -8245.998874
EM: Round [70] log likelihood: -8245.998696
EM: Round [71] log likelihood: -8245.998529
EM: Round [72] log likelihood: -8245.998374
EM: Round [73] log likelihood: -8245.998230
EM: Round [74] log likelihood: -8245.998095
EM: Round [75] log likelihood: -8245.997969
EM: Round [76] log likelihood: -8245.997851
EM: Round [77] log likelihood: -8245.997741
EM: Round [78] log likelihood: -8245.997639
EM: Round [79] log likelihood: -8245.997543
EM: Stopping iterations at round 79 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam into /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.read_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.71 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir
-done, see /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7999.183293
EM: Round [1] log likelihood: -7998.826244
EM: Round [2] log likelihood: -7998.607910
EM: Round [3] log likelihood: -7998.443077
EM: Round [4] log likelihood: -7998.318206
EM: Round [5] log likelihood: -7998.223551
EM: Round [6] log likelihood: -7998.151811
EM: Round [7] log likelihood: -7998.097478
EM: Round [8] log likelihood: -7998.056370
EM: Round [9] log likelihood: -7998.025307
EM: Round [10] log likelihood: -7998.001865
EM: Round [11] log likelihood: -7997.984200
EM: Round [12] log likelihood: -7997.970905
EM: Round [13] log likelihood: -7997.960912
EM: Round [14] log likelihood: -7997.953410
EM: Round [15] log likelihood: -7997.947785
EM: Round [16] log likelihood: -7997.943572
EM: Round [17] log likelihood: -7997.940419
EM: Round [18] log likelihood: -7997.938061
EM: Round [19] log likelihood: -7997.936299
EM: Round [20] log likelihood: -7997.934984
EM: Round [21] log likelihood: -7997.934003
EM: Round [22] log likelihood: -7997.933271
EM: Round [23] log likelihood: -7997.932725
EM: Round [24] log likelihood: -7997.932318
EM: Round [25] log likelihood: -7997.932015
EM: Round [26] log likelihood: -7997.931790
EM: Round [27] log likelihood: -7997.931622
EM: Round [28] log likelihood: -7997.931497
EM: Round [29] log likelihood: -7997.931404
EM: Stopping iterations at round 29 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz: 295807620
Execution Time = 5.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/fi_workdir/microH.dat
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.wrwpEnYaAa/fi_workdir/microH.dat /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa/fi_workdir/microH.dat /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.wrwpEnYaAa --json_outfile /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bst_02_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.wrwpEnYaAa --json_outfile /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1
Running: touch /tmp/nxf.wrwpEnYaAa/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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --html_output /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --html_output /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000235687.9]
WARNING, no entry stored in dbm for [ENSG00000224222.2]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000259543.1]
WARNING, no entry stored in dbm for [ENSG00000241860.7]
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 [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000232109.1]
WARNING, no entry stored in dbm for [ENSG00000232109.1]
WARNING, no entry stored in dbm for [ENSG00000255185.6]
WARNING, no entry stored in dbm for [ENSG00000255185.6]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000250039.4]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000253682.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory