Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/7bea8d0c2033f321f710e678d085f9/tih_rna_sample_00618_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/f37c087d81c291fefac97e2345e023/tih_rna_sample_00618_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/52e8177d3e4bf8731be7d0e6db4c73/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/52e8177d3e4bf8731be7d0e6db4c73/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/7bea8d0c2033f321f710e678d085f9/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00618_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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 tih_rna_sample_00618_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/cytoBand.txt
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00618_B23MVV7LT4_1.star --out_dir /tmp/nxf.4dBlDWtzDF/fi_workdir --reads "/tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:01:18 ..... started STAR run
Jun 08 10:01:18 ..... loading genome
Jun 08 10:03:00 ... generating Suffix Array index
Jun 08 10:06:44 ... completed Suffix Array index
Jun 08 10:06:44 ..... processing annotations GTF
Jun 08 10:06:45 ..... inserting junctions into the genome indices
Jun 08 10:07:45 ..... started mapping
Jun 08 11:05:18 ..... finished mapping
Jun 08 11:05:19 ..... started sorting BAM
Jun 08 11:05:21 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00618_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00618_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 64.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00618_B23MVV7LT4_1.star --out_dir /tmp/nxf.4dBlDWtzDF/fi_workdir --reads "/tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:05:43 : INFO : Done.
Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[3520000] -done parsing /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 96,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 152,
' ** passed ** ' => 25894,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 403,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 580,
'low complexity anchor region' => 27,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 21,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 27,
'exons hit < 2' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 230,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 44,
'small anchor length' => 247,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'num genes matched < 2' => 891,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 168,
'per_id < 96' => 9479,
'excessive soft clipping' => 15249,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'seq-similar region overlap' => 557
};
-writing fusion junction support info.
Execution Time = 1.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[84000] -fusion SPANNING read extraction for scaff: AC073264.3--TCAF1
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[524000] -fusion SPANNING read extraction for scaff: AL079338.1--LRRC41
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[524000] -fusion SPANNING read extraction for scaff: AL162718.1--LRRC41
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[14000] -fusion SPANNING read extraction for scaff: AL731769.2--SCART1
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[38000] -fusion SPANNING read extraction for scaff: BLACE--RHEX
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[529000] -fusion SPANNING read extraction for scaff: BX571818.1--LRRC41
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[38000] -fusion SPANNING read extraction for scaff: C4orf3--KLHL2
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[25000] -fusion SPANNING read extraction for scaff: GARS1-DT--GOLGA6L7
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[526000] -fusion SPANNING read extraction for scaff: LINC01320--LRRC41
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[52000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[52000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[55000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[52000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[52000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[55000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[50000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[83000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[60000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[34000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[84000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[61000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[32000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 14708,
'seq similar region alignment' => 145484
};
Execution Time = 4.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -9517.283975
EM: Round [1] log likelihood: -9508.365032
EM: Round [2] log likelihood: -9506.132478
EM: Round [3] log likelihood: -9504.392917
EM: Round [4] log likelihood: -9502.915749
EM: Round [5] log likelihood: -9501.632008
EM: Round [6] log likelihood: -9500.505084
EM: Round [7] log likelihood: -9499.508855
EM: Round [8] log likelihood: -9498.622775
EM: Round [9] log likelihood: -9497.830210
EM: Round [10] log likelihood: -9497.117541
EM: Round [11] log likelihood: -9496.473538
EM: Round [12] log likelihood: -9495.888888
EM: Round [13] log likelihood: -9495.355823
EM: Round [14] log likelihood: -9494.867825
EM: Round [15] log likelihood: -9494.419397
EM: Round [16] log likelihood: -9494.005883
EM: Round [17] log likelihood: -9493.623314
EM: Round [18] log likelihood: -9493.268296
EM: Round [19] log likelihood: -9492.937909
EM: Round [20] log likelihood: -9492.629636
EM: Round [21] log likelihood: -9492.341290
EM: Round [22] log likelihood: -9492.070971
EM: Round [23] log likelihood: -9491.817016
EM: Round [24] log likelihood: -9491.577965
EM: Round [25] log likelihood: -9491.352533
EM: Round [26] log likelihood: -9491.139582
EM: Round [27] log likelihood: -9490.938104
EM: Round [28] log likelihood: -9490.747198
EM: Round [29] log likelihood: -9490.566061
EM: Round [30] log likelihood: -9490.393971
EM: Round [31] log likelihood: -9490.230278
EM: Round [32] log likelihood: -9490.074396
EM: Round [33] log likelihood: -9489.925792
EM: Round [34] log likelihood: -9489.783984
EM: Round [35] log likelihood: -9489.648533
EM: Round [36] log likelihood: -9489.519035
EM: Round [37] log likelihood: -9489.395122
EM: Round [38] log likelihood: -9489.276456
EM: Round [39] log likelihood: -9489.162726
EM: Round [40] log likelihood: -9489.053645
EM: Round [41] log likelihood: -9488.948946
EM: Round [42] log likelihood: -9488.848384
EM: Round [43] log likelihood: -9488.751731
EM: Round [44] log likelihood: -9488.658774
EM: Round [45] log likelihood: -9488.569316
EM: Round [46] log likelihood: -9488.483173
EM: Round [47] log likelihood: -9488.400172
EM: Round [48] log likelihood: -9488.320152
EM: Round [49] log likelihood: -9488.242964
EM: Round [50] log likelihood: -9488.168465
EM: Round [51] log likelihood: -9488.096523
EM: Round [52] log likelihood: -9488.027014
EM: Round [53] log likelihood: -9487.959820
EM: Round [54] log likelihood: -9487.894832
EM: Round [55] log likelihood: -9487.831945
EM: Round [56] log likelihood: -9487.771061
EM: Round [57] log likelihood: -9487.712087
EM: Round [58] log likelihood: -9487.654938
EM: Round [59] log likelihood: -9487.599529
EM: Round [60] log likelihood: -9487.545784
EM: Round [61] log likelihood: -9487.493628
EM: Round [62] log likelihood: -9487.442991
EM: Round [63] log likelihood: -9487.393807
EM: Round [64] log likelihood: -9487.346013
EM: Round [65] log likelihood: -9487.299550
EM: Round [66] log likelihood: -9487.254362
EM: Round [67] log likelihood: -9487.210394
EM: Round [68] log likelihood: -9487.167596
EM: Round [69] log likelihood: -9487.125919
EM: Round [70] log likelihood: -9487.085317
EM: Round [71] log likelihood: -9487.045748
EM: Round [72] log likelihood: -9487.007168
EM: Round [73] log likelihood: -9486.969538
EM: Round [74] log likelihood: -9486.932822
EM: Round [75] log likelihood: -9486.896982
EM: Round [76] log likelihood: -9486.861985
EM: Round [77] log likelihood: -9486.827798
EM: Round [78] log likelihood: -9486.794390
EM: Round [79] log likelihood: -9486.761732
EM: Round [80] log likelihood: -9486.729795
EM: Round [81] log likelihood: -9486.698552
EM: Round [82] log likelihood: -9486.667978
EM: Round [83] log likelihood: -9486.638048
EM: Round [84] log likelihood: -9486.608738
EM: Round [85] log likelihood: -9486.580027
EM: Round [86] log likelihood: -9486.551892
EM: Round [87] log likelihood: -9486.524315
EM: Round [88] log likelihood: -9486.497274
EM: Round [89] log likelihood: -9486.470751
EM: Round [90] log likelihood: -9486.444728
EM: Round [91] log likelihood: -9486.419190
EM: Round [92] log likelihood: -9486.394118
EM: Round [93] log likelihood: -9486.369497
EM: Round [94] log likelihood: -9486.345313
EM: Round [95] log likelihood: -9486.321551
EM: Round [96] log likelihood: -9486.298197
EM: Round [97] log likelihood: -9486.275238
EM: Round [98] log likelihood: -9486.252662
EM: Round [99] log likelihood: -9486.230457
EM: Round [100] log likelihood: -9486.208610
EM: Round [101] log likelihood: -9486.187112
EM: Round [102] log likelihood: -9486.165951
EM: Round [103] log likelihood: -9486.145116
EM: Round [104] log likelihood: -9486.124599
EM: Round [105] log likelihood: -9486.104390
EM: Round [106] log likelihood: -9486.084480
EM: Round [107] log likelihood: -9486.064860
EM: Round [108] log likelihood: -9486.045522
EM: Round [109] log likelihood: -9486.026458
EM: Round [110] log likelihood: -9486.007660
EM: Round [111] log likelihood: -9485.989122
EM: Round [112] log likelihood: -9485.970834
EM: Round [113] log likelihood: -9485.952792
EM: Round [114] log likelihood: -9485.934989
EM: Round [115] log likelihood: -9485.917417
EM: Round [116] log likelihood: -9485.900072
EM: Round [117] log likelihood: -9485.882947
EM: Round [118] log likelihood: -9485.866036
EM: Round [119] log likelihood: -9485.849335
EM: Round [120] log likelihood: -9485.832838
EM: Round [121] log likelihood: -9485.816540
EM: Round [122] log likelihood: -9485.800436
EM: Round [123] log likelihood: -9485.784522
EM: Round [124] log likelihood: -9485.768793
EM: Round [125] log likelihood: -9485.753244
EM: Round [126] log likelihood: -9485.737873
EM: Round [127] log likelihood: -9485.722673
EM: Round [128] log likelihood: -9485.707643
EM: Round [129] log likelihood: -9485.692777
EM: Round [130] log likelihood: -9485.678073
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Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/tih_rna_sample_00618_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa > /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/tih_rna_sample_00618_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7103.752209
EM: Round [1] log likelihood: -7103.641192
EM: Round [2] log likelihood: -7103.576720
EM: Round [3] log likelihood: -7103.517433
EM: Round [4] log likelihood: -7103.462110
EM: Round [5] log likelihood: -7103.410418
EM: Round [6] log likelihood: -7103.362074
EM: Round [7] log likelihood: -7103.316817
EM: Round [8] log likelihood: -7103.274410
EM: Round [9] log likelihood: -7103.234635
EM: Round [10] log likelihood: -7103.197293
EM: Round [11] log likelihood: -7103.162200
EM: Round [12] log likelihood: -7103.129189
EM: Round [13] log likelihood: -7103.098104
EM: Round [14] log likelihood: -7103.068804
EM: Round [15] log likelihood: -7103.041156
EM: Round [16] log likelihood: -7103.015040
EM: Round [17] log likelihood: -7102.990345
EM: Round [18] log likelihood: -7102.966967
EM: Round [19] log likelihood: -7102.944811
EM: Round [20] log likelihood: -7102.923790
EM: Round [21] log likelihood: -7102.903822
EM: Round [22] log likelihood: -7102.884832
EM: Round [23] log likelihood: -7102.866751
EM: Round [24] log likelihood: -7102.849514
EM: Round [25] log likelihood: -7102.833063
EM: Round [26] log likelihood: -7102.817342
EM: Round [27] log likelihood: -7102.802300
EM: Round [28] log likelihood: -7102.787890
EM: Round [29] log likelihood: -7102.774068
EM: Round [30] log likelihood: -7102.760795
EM: Round [31] log likelihood: -7102.748032
EM: Round [32] log likelihood: -7102.735745
EM: Round [33] log likelihood: -7102.723902
EM: Round [34] log likelihood: -7102.712473
EM: Round [35] log likelihood: -7102.701430
EM: Round [36] log likelihood: -7102.690747
EM: Round [37] log likelihood: -7102.680402
EM: Round [38] log likelihood: -7102.670372
EM: Round [39] log likelihood: -7102.660636
EM: Round [40] log likelihood: -7102.651176
EM: Round [41] log likelihood: -7102.641975
EM: Round [42] log likelihood: -7102.633015
EM: Round [43] log likelihood: -7102.624283
EM: Round [44] log likelihood: -7102.615763
EM: Round [45] log likelihood: -7102.607443
EM: Round [46] log likelihood: -7102.599312
EM: Round [47] log likelihood: -7102.591357
EM: Round [48] log likelihood: -7102.583568
EM: Round [49] log likelihood: -7102.575937
EM: Round [50] log likelihood: -7102.568453
EM: Round [51] log likelihood: -7102.561110
EM: Round [52] log likelihood: -7102.553898
EM: Round [53] log likelihood: -7102.546811
EM: Round [54] log likelihood: -7102.539842
EM: Round [55] log likelihood: -7102.532986
EM: Round [56] log likelihood: -7102.526235
EM: Round [57] log likelihood: -7102.519586
EM: Round [58] log likelihood: -7102.513033
EM: Round [59] log likelihood: -7102.506572
EM: Round [60] log likelihood: -7102.500197
EM: Round [61] log likelihood: -7102.493906
EM: Round [62] log likelihood: -7102.487694
EM: Round [63] log likelihood: -7102.481559
EM: Round [64] log likelihood: -7102.475496
EM: Round [65] log likelihood: -7102.469503
EM: Round [66] log likelihood: -7102.463577
EM: Round [67] log likelihood: -7102.457716
EM: Round [68] log likelihood: -7102.451916
EM: Round [69] log likelihood: -7102.446176
EM: Round [70] log likelihood: -7102.440494
EM: Round [71] log likelihood: -7102.434867
EM: Round [72] log likelihood: -7102.429294
EM: Round [73] log likelihood: -7102.423773
EM: Round [74] log likelihood: -7102.418302
EM: Round [75] log likelihood: -7102.412879
EM: Round [76] log likelihood: -7102.407504
EM: Round [77] log likelihood: -7102.402175
EM: Round [78] log likelihood: -7102.396890
EM: Round [79] log likelihood: -7102.391649
EM: Round [80] log likelihood: -7102.386451
EM: Round [81] log likelihood: -7102.381293
EM: Round [82] log likelihood: -7102.376175
EM: Round [83] log likelihood: -7102.371097
EM: Round [84] log likelihood: -7102.366057
EM: Round [85] log likelihood: -7102.361055
EM: Round [86] log likelihood: -7102.356089
EM: Round [87] log likelihood: -7102.351160
EM: Round [88] log likelihood: -7102.346265
EM: Round [89] log likelihood: -7102.341405
EM: Round [90] log likelihood: -7102.336578
EM: Round [91] log likelihood: -7102.331785
EM: Round [92] log likelihood: -7102.327025
EM: Round [93] log likelihood: -7102.322296
EM: Round [94] log likelihood: -7102.317599
EM: Round [95] log likelihood: -7102.312933
EM: Round [96] log likelihood: -7102.308297
EM: Round [97] log likelihood: -7102.303691
EM: Round [98] log likelihood: -7102.299115
EM: Round [99] log likelihood: -7102.294567
EM: Round [100] log likelihood: -7102.290049
EM: Round [101] log likelihood: -7102.285558
EM: Round [102] log likelihood: -7102.281095
EM: Round [103] log likelihood: -7102.276660
EM: Round [104] log likelihood: -7102.272251
EM: Round [105] log likelihood: -7102.267870
EM: Round [106] log likelihood: -7102.263514
EM: Round [107] log likelihood: -7102.259185
EM: Round [108] log likelihood: -7102.254881
EM: Round [109] log likelihood: -7102.250603
EM: Round [110] log likelihood: -7102.246350
EM: Round [111] log likelihood: -7102.242121
EM: Round [112] log likelihood: -7102.237917
EM: Round [113] log likelihood: -7102.233737
EM: Round [114] log likelihood: -7102.229581
EM: Round [115] log likelihood: -7102.225448
EM: Round [116] log likelihood: -7102.221339
EM: Round [117] log likelihood: -7102.217253
EM: Round [118] log likelihood: -7102.213190
EM: Round [119] log likelihood: -7102.209149
EM: Round [120] log likelihood: -7102.205131
EM: Round [121] log likelihood: -7102.201135
EM: Round [122] log likelihood: -7102.197160
EM: Round [123] log likelihood: -7102.193208
EM: Round [124] log likelihood: -7102.189277
EM: Round [125] log likelihood: -7102.185367
EM: Round [126] log likelihood: -7102.181478
EM: Round [127] log likelihood: -7102.177610
EM: Round [128] log likelihood: -7102.173763
EM: Round [129] log likelihood: -7102.169936
EM: Round [130] log likelihood: -7102.166129
EM: Round [131] log likelihood: -7102.162343
EM: Round [132] log likelihood: -7102.158576
EM: Round [133] log likelihood: -7102.154828
EM: Round [134] log likelihood: -7102.151101
EM: Round [135] log likelihood: -7102.147392
EM: Round [136] log likelihood: -7102.143703
EM: Round [137] log likelihood: -7102.140033
EM: Round [138] log likelihood: -7102.136381
EM: Round [139] log likelihood: -7102.132748
EM: Round [140] log likelihood: -7102.129134
EM: Round [141] log likelihood: -7102.125537
EM: Round [142] log likelihood: -7102.121959
EM: Round [143] log likelihood: -7102.118399
EM: Round [144] log likelihood: -7102.114857
EM: Round [145] log likelihood: -7102.111332
EM: Round [146] log likelihood: -7102.107824
EM: Round [147] log likelihood: -7102.104335
EM: Round [148] log likelihood: -7102.100862
EM: Round [149] log likelihood: -7102.097406
EM: Round [150] log likelihood: -7102.093967
EM: Round [151] log likelihood: -7102.090545
EM: Round [152] log likelihood: -7102.087140
EM: Round [153] log likelihood: -7102.083751
EM: Round [154] log likelihood: -7102.080378
EM: Round [155] log likelihood: -7102.077022
EM: Round [156] log likelihood: -7102.073681
EM: Round [157] log likelihood: -7102.070357
EM: Round [158] log likelihood: -7102.067049
EM: Round [159] log likelihood: -7102.063756
EM: Round [160] log likelihood: -7102.060478
EM: Round [161] log likelihood: -7102.057216
EM: Round [162] log likelihood: -7102.053970
EM: Round [163] log likelihood: -7102.050739
EM: Round [164] log likelihood: -7102.047522
EM: Round [165] log likelihood: -7102.044321
EM: Round [166] log likelihood: -7102.041134
EM: Round [167] log likelihood: -7102.037963
EM: Round [168] log likelihood: -7102.034805
EM: Round [169] log likelihood: -7102.031663
EM: Round [170] log likelihood: -7102.028534
EM: Round [171] log likelihood: -7102.025420
EM: Round [172] log likelihood: -7102.022320
EM: Round [173] log likelihood: -7102.019234
EM: Round [174] log likelihood: -7102.016163
EM: Round [175] log likelihood: -7102.013104
EM: Round [176] log likelihood: -7102.010060
EM: Round [177] log likelihood: -7102.007029
EM: Round [178] log likelihood: -7102.004012
EM: Round [179] log likelihood: -7102.001008
EM: Round [180] log likelihood: -7101.998018
EM: Round [181] log likelihood: -7101.995041
EM: Round [182] log likelihood: -7101.992077
EM: Round [183] log likelihood: -7101.989126
EM: Round [184] log likelihood: -7101.986188
EM: Round [185] log likelihood: -7101.983262
EM: Round [186] log likelihood: -7101.980350
EM: Round [187] log likelihood: -7101.977450
EM: Round [188] log likelihood: -7101.974563
EM: Round [189] log likelihood: -7101.971688
EM: Round [190] log likelihood: -7101.968825
EM: Round [191] log likelihood: -7101.965975
EM: Round [192] log likelihood: -7101.963137
EM: Round [193] log likelihood: -7101.960311
EM: Round [194] log likelihood: -7101.957498
EM: Round [195] log likelihood: -7101.954696
EM: Round [196] log likelihood: -7101.951906
EM: Round [197] log likelihood: -7101.949128
EM: Round [198] log likelihood: -7101.946361
EM: Round [199] log likelihood: -7101.943606
EM: Round [200] log likelihood: -7101.940863
EM: Round [201] log likelihood: -7101.938131
EM: Round [202] log likelihood: -7101.935410
EM: Round [203] log likelihood: -7101.932701
EM: Round [204] log likelihood: -7101.930003
EM: Round [205] log likelihood: -7101.927316
EM: Round [206] log likelihood: -7101.924641
EM: Round [207] log likelihood: -7101.921976
EM: Round [208] log likelihood: -7101.919322
EM: Round [209] log likelihood: -7101.916679
EM: Round [210] log likelihood: -7101.914047
EM: Round [211] log likelihood: -7101.911426
EM: Round [212] log likelihood: -7101.908815
EM: Round [213] log likelihood: -7101.906214
EM: Round [214] log likelihood: -7101.903625
EM: Round [215] log likelihood: -7101.901045
EM: Round [216] log likelihood: -7101.898476
EM: Round [217] log likelihood: -7101.895917
EM: Round [218] log likelihood: -7101.893369
EM: Round [219] log likelihood: -7101.890831
EM: Round [220] log likelihood: -7101.888302
EM: Round [221] log likelihood: -7101.885784
EM: Round [222] log likelihood: -7101.883276
EM: Round [223] log likelihood: -7101.880777
EM: Round [224] log likelihood: -7101.878289
EM: Round [225] log likelihood: -7101.875810
EM: Round [226] log likelihood: -7101.873341
EM: Round [227] log likelihood: -7101.870881
EM: Round [228] log likelihood: -7101.868431
EM: Round [229] log likelihood: -7101.865991
EM: Round [230] log likelihood: -7101.863560
EM: Round [231] log likelihood: -7101.861139
EM: Round [232] log likelihood: -7101.858727
EM: Round [233] log likelihood: -7101.856324
EM: Round [234] log likelihood: -7101.853930
EM: Round [235] log likelihood: -7101.851545
EM: Round [236] log likelihood: -7101.849170
EM: Round [237] log likelihood: -7101.846804
EM: Round [238] log likelihood: -7101.844446
EM: Round [239] log likelihood: -7101.842098
EM: Round [240] log likelihood: -7101.839759
EM: Round [241] log likelihood: -7101.837428
EM: Round [242] log likelihood: -7101.835106
EM: Round [243] log likelihood: -7101.832793
EM: Round [244] log likelihood: -7101.830488
EM: Round [245] log likelihood: -7101.828193
EM: Round [246] log likelihood: -7101.825905
EM: Round [247] log likelihood: -7101.823626
EM: Round [248] log likelihood: -7101.821356
EM: Round [249] log likelihood: -7101.819094
EM: Round [250] log likelihood: -7101.816841
EM: Round [251] log likelihood: -7101.814596
EM: Round [252] log likelihood: -7101.812359
EM: Round [253] log likelihood: -7101.810130
EM: Round [254] log likelihood: -7101.807909
EM: Round [255] log likelihood: -7101.805697
EM: Round [256] log likelihood: -7101.803493
EM: Round [257] log likelihood: -7101.801296
EM: Round [258] log likelihood: -7101.799108
EM: Round [259] log likelihood: -7101.796928
EM: Round [260] log likelihood: -7101.794755
EM: Round [261] log likelihood: -7101.792590
EM: Round [262] log likelihood: -7101.790434
EM: Round [263] log likelihood: -7101.788284
EM: Round [264] log likelihood: -7101.786143
EM: Round [265] log likelihood: -7101.784009
EM: Round [266] log likelihood: -7101.781883
EM: Round [267] log likelihood: -7101.779765
EM: Round [268] log likelihood: -7101.777654
EM: Round [269] log likelihood: -7101.775550
EM: Round [270] log likelihood: -7101.773454
EM: Round [271] log likelihood: -7101.771365
EM: Round [272] log likelihood: -7101.769284
EM: Round [273] log likelihood: -7101.767210
EM: Round [274] log likelihood: -7101.765143
EM: Round [275] log likelihood: -7101.763084
EM: Round [276] log likelihood: -7101.761032
EM: Round [277] log likelihood: -7101.758987
EM: Round [278] log likelihood: -7101.756949
EM: Round [279] log likelihood: -7101.754918
EM: Round [280] log likelihood: -7101.752894
EM: Round [281] log likelihood: -7101.750877
EM: Round [282] log likelihood: -7101.748867
EM: Round [283] log likelihood: -7101.746865
EM: Round [284] log likelihood: -7101.744868
EM: Round [285] log likelihood: -7101.742879
EM: Round [286] log likelihood: -7101.740897
EM: Round [287] log likelihood: -7101.738921
EM: Round [288] log likelihood: -7101.736953
EM: Round [289] log likelihood: -7101.734991
EM: Round [290] log likelihood: -7101.733035
EM: Round [291] log likelihood: -7101.731086
EM: Round [292] log likelihood: -7101.729144
EM: Round [293] log likelihood: -7101.727209
EM: Round [294] log likelihood: -7101.725279
EM: Round [295] log likelihood: -7101.723357
EM: Round [296] log likelihood: -7101.721441
EM: Round [297] log likelihood: -7101.719531
EM: Round [298] log likelihood: -7101.717628
EM: Round [299] log likelihood: -7101.715731
EM: Round [300] log likelihood: -7101.713840
EM: Round [301] log likelihood: -7101.711956
EM: Round [302] log likelihood: -7101.710078
EM: Round [303] log likelihood: -7101.708206
EM: Round [304] log likelihood: -7101.706340
EM: Round [305] log likelihood: -7101.704481
EM: Round [306] log likelihood: -7101.702628
EM: Round [307] log likelihood: -7101.700780
EM: Round [308] log likelihood: -7101.698939
EM: Round [309] log likelihood: -7101.697104
EM: Round [310] log likelihood: -7101.695275
EM: Round [311] log likelihood: -7101.693452
EM: Round [312] log likelihood: -7101.691635
EM: Round [313] log likelihood: -7101.689824
EM: Round [314] log likelihood: -7101.688018
EM: Round [315] log likelihood: -7101.686219
EM: Round [316] log likelihood: -7101.684425
EM: Round [317] log likelihood: -7101.682637
EM: Round [318] log likelihood: -7101.680855
EM: Round [319] log likelihood: -7101.679079
EM: Round [320] log likelihood: -7101.677308
EM: Round [321] log likelihood: -7101.675543
EM: Round [322] log likelihood: -7101.673784
EM: Round [323] log likelihood: -7101.672030
EM: Round [324] log likelihood: -7101.670282
EM: Round [325] log likelihood: -7101.668540
EM: Round [326] log likelihood: -7101.666803
EM: Round [327] log likelihood: -7101.665071
EM: Round [328] log likelihood: -7101.663345
EM: Round [329] log likelihood: -7101.661625
EM: Round [330] log likelihood: -7101.659910
EM: Round [331] log likelihood: -7101.658200
EM: Round [332] log likelihood: -7101.656496
EM: Round [333] log likelihood: -7101.654797
EM: Round [334] log likelihood: -7101.653103
EM: Round [335] log likelihood: -7101.651415
EM: Round [336] log likelihood: -7101.649732
EM: Round [337] log likelihood: -7101.648055
EM: Round [338] log likelihood: -7101.646382
EM: Round [339] log likelihood: -7101.644715
EM: Round [340] log likelihood: -7101.643053
EM: Round [341] log likelihood: -7101.641396
EM: Round [342] log likelihood: -7101.639744
EM: Round [343] log likelihood: -7101.638097
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EM: Round [352] log likelihood: -7101.623503
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EM: Round [435] log likelihood: -7101.505652
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EM: Round [895] log likelihood: -7101.152672
EM: Round [896] log likelihood: -7101.152217
EM: Round [897] log likelihood: -7101.151763
EM: Round [898] log likelihood: -7101.151311
EM: Round [899] log likelihood: -7101.150859
EM: Round [900] log likelihood: -7101.150408
EM: Round [901] log likelihood: -7101.149958
EM: Round [902] log likelihood: -7101.149508
EM: Round [903] log likelihood: -7101.149060
EM: Round [904] log likelihood: -7101.148612
EM: Round [905] log likelihood: -7101.148165
EM: Round [906] log likelihood: -7101.147719
EM: Round [907] log likelihood: -7101.147274
EM: Round [908] log likelihood: -7101.146830
EM: Round [909] log likelihood: -7101.146387
EM: Round [910] log likelihood: -7101.145944
EM: Round [911] log likelihood: -7101.145502
EM: Round [912] log likelihood: -7101.145061
EM: Round [913] log likelihood: -7101.144621
EM: Round [914] log likelihood: -7101.144182
EM: Round [915] log likelihood: -7101.143744
EM: Round [916] log likelihood: -7101.143306
EM: Round [917] log likelihood: -7101.142869
EM: Round [918] log likelihood: -7101.142433
EM: Round [919] log likelihood: -7101.141998
EM: Round [920] log likelihood: -7101.141564
EM: Round [921] log likelihood: -7101.141130
EM: Round [922] log likelihood: -7101.140698
EM: Round [923] log likelihood: -7101.140266
EM: Round [924] log likelihood: -7101.139835
EM: Round [925] log likelihood: -7101.139405
EM: Round [926] log likelihood: -7101.138975
EM: Round [927] log likelihood: -7101.138547
EM: Round [928] log likelihood: -7101.138119
EM: Round [929] log likelihood: -7101.137692
EM: Round [930] log likelihood: -7101.137265
EM: Round [931] log likelihood: -7101.136840
EM: Round [932] log likelihood: -7101.136415
EM: Round [933] log likelihood: -7101.135992
EM: Round [934] log likelihood: -7101.135569
EM: Round [935] log likelihood: -7101.135146
EM: Round [936] log likelihood: -7101.134725
EM: Round [937] log likelihood: -7101.134304
EM: Round [938] log likelihood: -7101.133884
EM: Round [939] log likelihood: -7101.133465
EM: Round [940] log likelihood: -7101.133047
EM: Round [941] log likelihood: -7101.132629
EM: Round [942] log likelihood: -7101.132212
EM: Round [943] log likelihood: -7101.131797
EM: Round [944] log likelihood: -7101.131381
EM: Round [945] log likelihood: -7101.130967
EM: Round [946] log likelihood: -7101.130553
EM: Round [947] log likelihood: -7101.130140
EM: Round [948] log likelihood: -7101.129728
EM: Round [949] log likelihood: -7101.129317
EM: Round [950] log likelihood: -7101.128906
EM: Round [951] log likelihood: -7101.128496
EM: Round [952] log likelihood: -7101.128087
EM: Round [953] log likelihood: -7101.127679
EM: Round [954] log likelihood: -7101.127271
EM: Round [955] log likelihood: -7101.126865
EM: Round [956] log likelihood: -7101.126458
EM: Round [957] log likelihood: -7101.126053
EM: Round [958] log likelihood: -7101.125649
EM: Round [959] log likelihood: -7101.125245
EM: Round [960] log likelihood: -7101.124842
EM: Round [961] log likelihood: -7101.124439
EM: Round [962] log likelihood: -7101.124038
EM: Round [963] log likelihood: -7101.123637
EM: Round [964] log likelihood: -7101.123237
EM: Round [965] log likelihood: -7101.122838
EM: Round [966] log likelihood: -7101.122439
EM: Round [967] log likelihood: -7101.122041
EM: Round [968] log likelihood: -7101.121644
EM: Round [969] log likelihood: -7101.121248
EM: Round [970] log likelihood: -7101.120852
EM: Round [971] log likelihood: -7101.120457
EM: Round [972] log likelihood: -7101.120063
EM: Round [973] log likelihood: -7101.119669
EM: Round [974] log likelihood: -7101.119276
EM: Round [975] log likelihood: -7101.118884
EM: Round [976] log likelihood: -7101.118493
EM: Round [977] log likelihood: -7101.118102
EM: Round [978] log likelihood: -7101.117713
EM: Round [979] log likelihood: -7101.117323
EM: Round [980] log likelihood: -7101.116935
EM: Round [981] log likelihood: -7101.116547
EM: Round [982] log likelihood: -7101.116160
EM: Round [983] log likelihood: -7101.115774
EM: Round [984] log likelihood: -7101.115388
EM: Round [985] log likelihood: -7101.115003
EM: Round [986] log likelihood: -7101.114619
EM: Round [987] log likelihood: -7101.114235
EM: Round [988] log likelihood: -7101.113853
EM: Round [989] log likelihood: -7101.113471
EM: Round [990] log likelihood: -7101.113089
EM: Round [991] log likelihood: -7101.112708
EM: Round [992] log likelihood: -7101.112328
EM: Round [993] log likelihood: -7101.111949
EM: Round [994] log likelihood: -7101.111570
EM: Round [995] log likelihood: -7101.111193
EM: Round [996] log likelihood: -7101.110815
EM: Round [997] log likelihood: -7101.110439
EM: Round [998] log likelihood: -7101.110063
EM: Round [999] log likelihood: -7101.109688
EM: Round [1000] log likelihood: -7101.109313
EM: Round [1001] log likelihood: -7101.108939
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz: 296121221
Execution Time = 5.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa --gtf /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fa --gtf /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.gtf > /tmp/nxf.4dBlDWtzDF/fi_workdir/microH.dat
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4dBlDWtzDF/fi_workdir/microH.dat /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/fi_workdir/microH.dat /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4dBlDWtzDF --json_outfile /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00618_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4dBlDWtzDF --json_outfile /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00618_B23MVV7LT4_1
Running: touch /tmp/nxf.4dBlDWtzDF/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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00618_B23MVV7LT4_1 --html_output /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_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.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00618_B23MVV7LT4_1 --html_output /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000285417.1]
WARNING, no entry stored in dbm for [ENSG00000196295.12]
WARNING, no entry stored in dbm for [ENSG00000196295.12]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000288107.1]
WARNING, no entry stored in dbm for [ENSG00000283537.2]
WARNING, no entry stored in dbm for [ENSG00000283537.2]
WARNING, no entry stored in dbm for [ENSG00000283537.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4dBlDWtzDF/ctat_genome_lib_build_dir > /tmp/nxf.4dBlDWtzDF/tih_rna_sample_00618_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.4dBlDWtzDF/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory