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/64/a7c5d0a5487e3cd2319087951e468e/tih_rna_sample_00641_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/bef731c6afe634b10cc1857db9bcbc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/bef731c6afe634b10cc1857db9bcbc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/ddda0d89a9267d237cddaf9fa66a2c/tih_rna_sample_00641_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/ddda0d89a9267d237cddaf9fa66a2c/tih_rna_sample_00641_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_00641_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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_00641_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/cytoBand.txt
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00641_B23MVV7LT4_1.star --out_dir /tmp/nxf.UDv895oNsM/fi_workdir --reads "/tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.UDv895oNsM/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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:27:19 ..... started STAR run
Jun 08 10:27:19 ..... loading genome
Jun 08 10:29:06 ... generating Suffix Array index
Jun 08 10:32:57 ... completed Suffix Array index
Jun 08 10:32:57 ..... processing annotations GTF
Jun 08 10:32:57 ..... inserting junctions into the genome indices
Jun 08 10:33:58 ..... started mapping
Jun 08 11:55:03 ..... finished mapping
Jun 08 11:55:05 ..... started sorting BAM
Jun 08 11:55:13 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00641_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00641_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 88.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00641_B23MVV7LT4_1.star --out_dir /tmp/nxf.UDv895oNsM/fi_workdir --reads "/tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:56:30 : INFO : Done.
Execution Time = 1.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[11730000] -done parsing /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 63,
'small anchor length' => 13,
'exons hit < 2' => 2,
'seq-similar region overlap' => 1260,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 102,
'per_id < 96' => 41003,
' ** passed ** ' => 8406,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 107,
'low complexity anchor region' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 57,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 164,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1470,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 860,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 62268
};
-writing fusion junction support info.
Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
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[6000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[13000] -fusion SPANNING read extraction for scaff: AC079781.4--ASNS
[1000]
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[12000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[597000] -fusion SPANNING read extraction for scaff: ACTBP6--ACTB
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[10000] -fusion SPANNING read extraction for scaff: CST9--CST9L
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[1036000] -fusion SPANNING read extraction for scaff: EIF4EBP1--NSD3
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[36000] -fusion SPANNING read extraction for scaff: EIF4EBP1--EYS
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[4805000] -fusion SPANNING read extraction for scaff: FGFR1--AC069120.1
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[83000] -fusion SPANNING read extraction for scaff: H2AC18--H3C13
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[421000] -fusion SPANNING read extraction for scaff: IKBKB--AL121949.1
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[421000] -fusion SPANNING read extraction for scaff: IKBKB--EEF1B2P5
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[3000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[46000] -fusion SPANNING read extraction for scaff: NOL4L--PDRG1
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[41000] -fusion SPANNING read extraction for scaff: NOL4L--XKR7
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[1058000] -fusion SPANNING read extraction for scaff: NSD3--EYS
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[1028000] -fusion SPANNING read extraction for scaff: NSD3--SMARCE1P4
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[1020000]
[1021000]
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[1024000]
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[1026000]
[1027000]
[1028000] -fusion SPANNING read extraction for scaff: NSD3--AC091182.1
[1000]
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[36000]
[37000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[1000]
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[37000]
[38000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
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[41000]
[42000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
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[47000] -fusion SPANNING read extraction for scaff: PLEKHA2--AL355375.2
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[47000] -fusion SPANNING read extraction for scaff: PLEKHA2--AL450346.1
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[484000] -fusion SPANNING read extraction for scaff: RAB11FIP1--ADAM5
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[79000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[78000] -fusion SPANNING read extraction for scaff: TCF4--HNRNPA1P57
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[29000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[103000] -fusion SPANNING read extraction for scaff: TTC6--AL132857.1
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[30000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[22000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
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[29000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 80511,
'seq similar region alignment' => 71880
};
Execution Time = 19.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -13786.406391
EM: Round [1] log likelihood: -13774.382245
EM: Round [2] log likelihood: -13773.934596
EM: Round [3] log likelihood: -13773.576685
EM: Round [4] log likelihood: -13773.244906
EM: Round [5] log likelihood: -13772.936691
EM: Round [6] log likelihood: -13772.650030
EM: Round [7] log likelihood: -13772.383130
EM: Round [8] log likelihood: -13772.134383
EM: Round [9] log likelihood: -13771.902344
EM: Round [10] log likelihood: -13771.685706
EM: Round [11] log likelihood: -13771.483288
EM: Round [12] log likelihood: -13771.294018
EM: Round [13] log likelihood: -13771.116919
EM: Round [14] log likelihood: -13770.951102
EM: Round [15] log likelihood: -13770.795753
EM: Round [16] log likelihood: -13770.650127
EM: Round [17] log likelihood: -13770.513540
EM: Round [18] log likelihood: -13770.385365
EM: Round [19] log likelihood: -13770.265023
EM: Round [20] log likelihood: -13770.151981
EM: Round [21] log likelihood: -13770.045747
EM: Round [22] log likelihood: -13769.945866
EM: Round [23] log likelihood: -13769.851918
EM: Round [24] log likelihood: -13769.763513
EM: Round [25] log likelihood: -13769.680290
EM: Round [26] log likelihood: -13769.601912
EM: Round [27] log likelihood: -13769.528069
EM: Round [28] log likelihood: -13769.458470
EM: Round [29] log likelihood: -13769.392846
EM: Round [30] log likelihood: -13769.330947
EM: Round [31] log likelihood: -13769.272537
EM: Round [32] log likelihood: -13769.217398
EM: Round [33] log likelihood: -13769.165328
EM: Round [34] log likelihood: -13769.116137
EM: Round [35] log likelihood: -13769.069645
EM: Round [36] log likelihood: -13769.025689
EM: Round [37] log likelihood: -13768.984113
EM: Round [38] log likelihood: -13768.944771
EM: Round [39] log likelihood: -13768.907529
EM: Round [40] log likelihood: -13768.872258
EM: Round [41] log likelihood: -13768.838841
EM: Round [42] log likelihood: -13768.807165
EM: Round [43] log likelihood: -13768.777127
EM: Round [44] log likelihood: -13768.748628
EM: Round [45] log likelihood: -13768.721577
EM: Round [46] log likelihood: -13768.695888
EM: Round [47] log likelihood: -13768.671479
EM: Round [48] log likelihood: -13768.648276
EM: Round [49] log likelihood: -13768.626207
EM: Round [50] log likelihood: -13768.605206
EM: Round [51] log likelihood: -13768.585209
EM: Round [52] log likelihood: -13768.566158
EM: Round [53] log likelihood: -13768.547998
EM: Round [54] log likelihood: -13768.530677
EM: Round [55] log likelihood: -13768.514146
EM: Round [56] log likelihood: -13768.498359
EM: Round [57] log likelihood: -13768.483273
EM: Round [58] log likelihood: -13768.468848
EM: Round [59] log likelihood: -13768.455046
EM: Round [60] log likelihood: -13768.441831
EM: Round [61] log likelihood: -13768.429169
EM: Round [62] log likelihood: -13768.417029
EM: Round [63] log likelihood: -13768.405380
EM: Round [64] log likelihood: -13768.394196
EM: Round [65] log likelihood: -13768.383449
EM: Round [66] log likelihood: -13768.373115
EM: Round [67] log likelihood: -13768.363171
EM: Round [68] log likelihood: -13768.353594
EM: Round [69] log likelihood: -13768.344365
EM: Round [70] log likelihood: -13768.335463
EM: Round [71] log likelihood: -13768.326870
EM: Round [72] log likelihood: -13768.318570
EM: Round [73] log likelihood: -13768.310546
EM: Round [74] log likelihood: -13768.302783
EM: Round [75] log likelihood: -13768.295266
EM: Round [76] log likelihood: -13768.287982
EM: Round [77] log likelihood: -13768.280918
EM: Round [78] log likelihood: -13768.274063
EM: Round [79] log likelihood: -13768.267404
EM: Round [80] log likelihood: -13768.260933
EM: Round [81] log likelihood: -13768.254637
EM: Round [82] log likelihood: -13768.248509
EM: Round [83] log likelihood: -13768.242539
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EM: Round [1000] log likelihood: -13767.272436
EM: Round [1001] log likelihood: -13767.272272
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/tih_rna_sample_00641_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 3.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa > /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/tih_rna_sample_00641_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir
-done, see /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -12921.934006
EM: Round [1] log likelihood: -12917.240847
EM: Round [2] log likelihood: -12917.200538
EM: Round [3] log likelihood: -12917.194578
EM: Round [4] log likelihood: -12917.188927
EM: Round [5] log likelihood: -12917.183310
EM: Round [6] log likelihood: -12917.177725
EM: Round [7] log likelihood: -12917.172172
EM: Round [8] log likelihood: -12917.166651
EM: Round [9] log likelihood: -12917.161160
EM: Round [10] log likelihood: -12917.155700
EM: Round [11] log likelihood: -12917.150271
EM: Round [12] log likelihood: -12917.144873
EM: Round [13] log likelihood: -12917.139504
EM: Round [14] log likelihood: -12917.134165
EM: Round [15] log likelihood: -12917.128856
EM: Round [16] log likelihood: -12917.123576
EM: Round [17] log likelihood: -12917.118325
EM: Round [18] log likelihood: -12917.113104
EM: Round [19] log likelihood: -12917.107910
EM: Round [20] log likelihood: -12917.102746
EM: Round [21] log likelihood: -12917.097609
EM: Round [22] log likelihood: -12917.092501
EM: Round [23] log likelihood: -12917.087420
EM: Round [24] log likelihood: -12917.082366
EM: Round [25] log likelihood: -12917.077340
EM: Round [26] log likelihood: -12917.072342
EM: Round [27] log likelihood: -12917.067369
EM: Round [28] log likelihood: -12917.062424
EM: Round [29] log likelihood: -12917.057505
EM: Round [30] log likelihood: -12917.052613
EM: Round [31] log likelihood: -12917.047746
EM: Round [32] log likelihood: -12917.042905
EM: Round [33] log likelihood: -12917.038090
EM: Round [34] log likelihood: -12917.033300
EM: Round [35] log likelihood: -12917.028536
EM: Round [36] log likelihood: -12917.023797
EM: Round [37] log likelihood: -12917.019082
EM: Round [38] log likelihood: -12917.014392
EM: Round [39] log likelihood: -12917.009727
EM: Round [40] log likelihood: -12917.005086
EM: Round [41] log likelihood: -12917.000469
EM: Round [42] log likelihood: -12916.995876
EM: Round [43] log likelihood: -12916.991307
EM: Round [44] log likelihood: -12916.986762
EM: Round [45] log likelihood: -12916.982240
EM: Round [46] log likelihood: -12916.977741
EM: Round [47] log likelihood: -12916.973265
EM: Round [48] log likelihood: -12916.968812
EM: Round [49] log likelihood: -12916.964382
EM: Round [50] log likelihood: -12916.959975
EM: Round [51] log likelihood: -12916.955589
EM: Round [52] log likelihood: -12916.951226
EM: Round [53] log likelihood: -12916.946886
EM: Round [54] log likelihood: -12916.942567
EM: Round [55] log likelihood: -12916.938270
EM: Round [56] log likelihood: -12916.933994
EM: Round [57] log likelihood: -12916.929740
EM: Round [58] log likelihood: -12916.925507
EM: Round [59] log likelihood: -12916.921296
EM: Round [60] log likelihood: -12916.917105
EM: Round [61] log likelihood: -12916.912935
EM: Round [62] log likelihood: -12916.908786
EM: Round [63] log likelihood: -12916.904658
EM: Round [64] log likelihood: -12916.900549
EM: Round [65] log likelihood: -12916.896462
EM: Round [66] log likelihood: -12916.892394
EM: Round [67] log likelihood: -12916.888346
EM: Round [68] log likelihood: -12916.884318
EM: Round [69] log likelihood: -12916.880310
EM: Round [70] log likelihood: -12916.876322
EM: Round [71] log likelihood: -12916.872353
EM: Round [72] log likelihood: -12916.868403
EM: Round [73] log likelihood: -12916.864472
EM: Round [74] log likelihood: -12916.860561
EM: Round [75] log likelihood: -12916.856668
EM: Round [76] log likelihood: -12916.852795
EM: Round [77] log likelihood: -12916.848939
EM: Round [78] log likelihood: -12916.845103
EM: Round [79] log likelihood: -12916.841285
EM: Round [80] log likelihood: -12916.837485
EM: Round [81] log likelihood: -12916.833703
EM: Round [82] log likelihood: -12916.829939
EM: Round [83] log likelihood: -12916.826194
EM: Round [84] log likelihood: -12916.822466
EM: Round [85] log likelihood: -12916.818755
EM: Round [86] log likelihood: -12916.815063
EM: Round [87] log likelihood: -12916.811388
EM: Round [88] log likelihood: -12916.807730
EM: Round [89] log likelihood: -12916.804089
EM: Round [90] log likelihood: -12916.800466
EM: Round [91] log likelihood: -12916.796859
EM: Round [92] log likelihood: -12916.793270
EM: Round [93] log likelihood: -12916.789697
EM: Round [94] log likelihood: -12916.786141
EM: Round [95] log likelihood: -12916.782601
EM: Round [96] log likelihood: -12916.779078
EM: Round [97] log likelihood: -12916.775572
EM: Round [98] log likelihood: -12916.772081
EM: Round [99] log likelihood: -12916.768607
EM: Round [100] log likelihood: -12916.765149
EM: Round [101] log likelihood: -12916.761707
EM: Round [102] log likelihood: -12916.758280
EM: Round [103] log likelihood: -12916.754870
EM: Round [104] log likelihood: -12916.751475
EM: Round [105] log likelihood: -12916.748095
EM: Round [106] log likelihood: -12916.744731
EM: Round [107] log likelihood: -12916.741383
EM: Round [108] log likelihood: -12916.738049
EM: Round [109] log likelihood: -12916.734731
EM: Round [110] log likelihood: -12916.731428
EM: Round [111] log likelihood: -12916.728140
EM: Round [112] log likelihood: -12916.724867
EM: Round [113] log likelihood: -12916.721608
EM: Round [114] log likelihood: -12916.718365
EM: Round [115] log likelihood: -12916.715135
EM: Round [116] log likelihood: -12916.711921
EM: Round [117] log likelihood: -12916.708721
EM: Round [118] log likelihood: -12916.705535
EM: Round [119] log likelihood: -12916.702363
EM: Round [120] log likelihood: -12916.699206
EM: Round [121] log likelihood: -12916.696063
EM: Round [122] log likelihood: -12916.692934
EM: Round [123] log likelihood: -12916.689818
EM: Round [124] log likelihood: -12916.686717
EM: Round [125] log likelihood: -12916.683629
EM: Round [126] log likelihood: -12916.680555
EM: Round [127] log likelihood: -12916.677495
EM: Round [128] log likelihood: -12916.674448
EM: Round [129] log likelihood: -12916.671414
EM: Round [130] log likelihood: -12916.668394
EM: Round [131] log likelihood: -12916.665387
EM: Round [132] log likelihood: -12916.662394
EM: Round [133] log likelihood: -12916.659413
EM: Round [134] log likelihood: -12916.656446
EM: Round [135] log likelihood: -12916.653491
EM: Round [136] log likelihood: -12916.650549
EM: Round [137] log likelihood: -12916.647621
EM: Round [138] log likelihood: -12916.644704
EM: Round [139] log likelihood: -12916.641801
EM: Round [140] log likelihood: -12916.638910
EM: Round [141] log likelihood: -12916.636032
EM: Round [142] log likelihood: -12916.633166
EM: Round [143] log likelihood: -12916.630313
EM: Round [144] log likelihood: -12916.627471
EM: Round [145] log likelihood: -12916.624642
EM: Round [146] log likelihood: -12916.621826
EM: Round [147] log likelihood: -12916.619021
EM: Round [148] log likelihood: -12916.616228
EM: Round [149] log likelihood: -12916.613448
EM: Round [150] log likelihood: -12916.610679
EM: Round [151] log likelihood: -12916.607922
EM: Round [152] log likelihood: -12916.605177
EM: Round [153] log likelihood: -12916.602443
EM: Round [154] log likelihood: -12916.599721
EM: Round [155] log likelihood: -12916.597011
EM: Round [156] log likelihood: -12916.594312
EM: Round [157] log likelihood: -12916.591625
EM: Round [158] log likelihood: -12916.588949
EM: Round [159] log likelihood: -12916.586284
EM: Round [160] log likelihood: -12916.583631
EM: Round [161] log likelihood: -12916.580988
EM: Round [162] log likelihood: -12916.578357
EM: Round [163] log likelihood: -12916.575737
EM: Round [164] log likelihood: -12916.573128
EM: Round [165] log likelihood: -12916.570530
EM: Round [166] log likelihood: -12916.567942
EM: Round [167] log likelihood: -12916.565366
EM: Round [168] log likelihood: -12916.562800
EM: Round [169] log likelihood: -12916.560245
EM: Round [170] log likelihood: -12916.557701
EM: Round [171] log likelihood: -12916.555167
EM: Round [172] log likelihood: -12916.552643
EM: Round [173] log likelihood: -12916.550131
EM: Round [174] log likelihood: -12916.547628
EM: Round [175] log likelihood: -12916.545136
EM: Round [176] log likelihood: -12916.542654
EM: Round [177] log likelihood: -12916.540183
EM: Round [178] log likelihood: -12916.537722
EM: Round [179] log likelihood: -12916.535270
EM: Round [180] log likelihood: -12916.532829
EM: Round [181] log likelihood: -12916.530398
EM: Round [182] log likelihood: -12916.527977
EM: Round [183] log likelihood: -12916.525566
EM: Round [184] log likelihood: -12916.523165
EM: Round [185] log likelihood: -12916.520773
EM: Round [186] log likelihood: -12916.518392
EM: Round [187] log likelihood: -12916.516020
EM: Round [188] log likelihood: -12916.513657
EM: Round [189] log likelihood: -12916.511304
EM: Round [190] log likelihood: -12916.508961
EM: Round [191] log likelihood: -12916.506628
EM: Round [192] log likelihood: -12916.504303
EM: Round [193] log likelihood: -12916.501989
EM: Round [194] log likelihood: -12916.499683
EM: Round [195] log likelihood: -12916.497387
EM: Round [196] log likelihood: -12916.495100
EM: Round [197] log likelihood: -12916.492823
EM: Round [198] log likelihood: -12916.490554
EM: Round [199] log likelihood: -12916.488295
EM: Round [200] log likelihood: -12916.486045
EM: Round [201] log likelihood: -12916.483803
EM: Round [202] log likelihood: -12916.481571
EM: Round [203] log likelihood: -12916.479348
EM: Round [204] log likelihood: -12916.477134
EM: Round [205] log likelihood: -12916.474928
EM: Round [206] log likelihood: -12916.472731
EM: Round [207] log likelihood: -12916.470543
EM: Round [208] log likelihood: -12916.468364
EM: Round [209] log likelihood: -12916.466193
EM: Round [210] log likelihood: -12916.464031
EM: Round [211] log likelihood: -12916.461878
EM: Round [212] log likelihood: -12916.459733
EM: Round [213] log likelihood: -12916.457597
EM: Round [214] log likelihood: -12916.455469
EM: Round [215] log likelihood: -12916.453349
EM: Round [216] log likelihood: -12916.451238
EM: Round [217] log likelihood: -12916.449136
EM: Round [218] log likelihood: -12916.447041
EM: Round [219] log likelihood: -12916.444955
EM: Round [220] log likelihood: -12916.442877
EM: Round [221] log likelihood: -12916.440807
EM: Round [222] log likelihood: -12916.438745
EM: Round [223] log likelihood: -12916.436691
EM: Round [224] log likelihood: -12916.434646
EM: Round [225] log likelihood: -12916.432608
EM: Round [226] log likelihood: -12916.430578
EM: Round [227] log likelihood: -12916.428556
EM: Round [228] log likelihood: -12916.426543
EM: Round [229] log likelihood: -12916.424537
EM: Round [230] log likelihood: -12916.422538
EM: Round [231] log likelihood: -12916.420548
EM: Round [232] log likelihood: -12916.418565
EM: Round [233] log likelihood: -12916.416590
EM: Round [234] log likelihood: -12916.414623
EM: Round [235] log likelihood: -12916.412663
EM: Round [236] log likelihood: -12916.410711
EM: Round [237] log likelihood: -12916.408766
EM: Round [238] log likelihood: -12916.406829
EM: Round [239] log likelihood: -12916.404899
EM: Round [240] log likelihood: -12916.402977
EM: Round [241] log likelihood: -12916.401062
EM: Round [242] log likelihood: -12916.399155
EM: Round [243] log likelihood: -12916.397255
EM: Round [244] log likelihood: -12916.395362
EM: Round [245] log likelihood: -12916.393476
EM: Round [246] log likelihood: -12916.391598
EM: Round [247] log likelihood: -12916.389727
EM: Round [248] log likelihood: -12916.387863
EM: Round [249] log likelihood: -12916.386006
EM: Round [250] log likelihood: -12916.384156
EM: Round [251] log likelihood: -12916.382314
EM: Round [252] log likelihood: -12916.380478
EM: Round [253] log likelihood: -12916.378649
EM: Round [254] log likelihood: -12916.376827
EM: Round [255] log likelihood: -12916.375013
EM: Round [256] log likelihood: -12916.373205
EM: Round [257] log likelihood: -12916.371403
EM: Round [258] log likelihood: -12916.369609
EM: Round [259] log likelihood: -12916.367822
EM: Round [260] log likelihood: -12916.366041
EM: Round [261] log likelihood: -12916.364267
EM: Round [262] log likelihood: -12916.362500
EM: Round [263] log likelihood: -12916.360739
EM: Round [264] log likelihood: -12916.358985
EM: Round [265] log likelihood: -12916.357238
EM: Round [266] log likelihood: -12916.355497
EM: Round [267] log likelihood: -12916.353763
EM: Round [268] log likelihood: -12916.352035
EM: Round [269] log likelihood: -12916.350314
EM: Round [270] log likelihood: -12916.348599
EM: Round [271] log likelihood: -12916.346891
EM: Round [272] log likelihood: -12916.345189
EM: Round [273] log likelihood: -12916.343493
EM: Round [274] log likelihood: -12916.341804
EM: Round [275] log likelihood: -12916.340121
EM: Round [276] log likelihood: -12916.338444
EM: Round [277] log likelihood: -12916.336774
EM: Round [278] log likelihood: -12916.335110
EM: Round [279] log likelihood: -12916.333452
EM: Round [280] log likelihood: -12916.331800
EM: Round [281] log likelihood: -12916.330154
EM: Round [282] log likelihood: -12916.328515
EM: Round [283] log likelihood: -12916.326881
EM: Round [284] log likelihood: -12916.325254
EM: Round [285] log likelihood: -12916.323632
EM: Round [286] log likelihood: -12916.322017
EM: Round [287] log likelihood: -12916.320408
EM: Round [288] log likelihood: -12916.318804
EM: Round [289] log likelihood: -12916.317207
EM: Round [290] log likelihood: -12916.315615
EM: Round [291] log likelihood: -12916.314029
EM: Round [292] log likelihood: -12916.312449
EM: Round [293] log likelihood: -12916.310875
EM: Round [294] log likelihood: -12916.309307
EM: Round [295] log likelihood: -12916.307744
EM: Round [296] log likelihood: -12916.306187
EM: Round [297] log likelihood: -12916.304636
EM: Round [298] log likelihood: -12916.303091
EM: Round [299] log likelihood: -12916.301551
EM: Round [300] log likelihood: -12916.300017
EM: Round [301] log likelihood: -12916.298488
EM: Round [302] log likelihood: -12916.296965
EM: Round [303] log likelihood: -12916.295448
EM: Round [304] log likelihood: -12916.293936
EM: Round [305] log likelihood: -12916.292429
EM: Round [306] log likelihood: -12916.290928
EM: Round [307] log likelihood: -12916.289433
EM: Round [308] log likelihood: -12916.287943
EM: Round [309] log likelihood: -12916.286459
EM: Round [310] log likelihood: -12916.284979
EM: Round [311] log likelihood: -12916.283506
EM: Round [312] log likelihood: -12916.282037
EM: Round [313] log likelihood: -12916.280574
EM: Round [314] log likelihood: -12916.279116
EM: Round [315] log likelihood: -12916.277664
EM: Round [316] log likelihood: -12916.276216
EM: Round [317] log likelihood: -12916.274774
EM: Round [318] log likelihood: -12916.273338
EM: Round [319] log likelihood: -12916.271906
EM: Round [320] log likelihood: -12916.270479
EM: Round [321] log likelihood: -12916.269058
EM: Round [322] log likelihood: -12916.267642
EM: Round [323] log likelihood: -12916.266231
EM: Round [324] log likelihood: -12916.264825
EM: Round [325] log likelihood: -12916.263424
EM: Round [326] log likelihood: -12916.262028
EM: Round [327] log likelihood: -12916.260637
EM: Round [328] log likelihood: -12916.259251
EM: Round [329] log likelihood: -12916.257870
EM: Round [330] log likelihood: -12916.256494
EM: Round [331] log likelihood: -12916.255122
EM: Round [332] log likelihood: -12916.253756
EM: Round [333] log likelihood: -12916.252395
EM: Round [334] log likelihood: -12916.251038
EM: Round [335] log likelihood: -12916.249687
EM: Round [336] log likelihood: -12916.248340
EM: Round [337] log likelihood: -12916.246998
EM: Round [338] log likelihood: -12916.245661
EM: Round [339] log likelihood: -12916.244328
EM: Round [340] log likelihood: -12916.243000
EM: Round [341] log likelihood: -12916.241677
EM: Round [342] log likelihood: -12916.240359
EM: Round [343] log likelihood: -12916.239045
EM: Round [344] log likelihood: -12916.237736
EM: Round [345] log likelihood: -12916.236432
EM: Round [346] log likelihood: -12916.235132
EM: Round [347] log likelihood: -12916.233837
EM: Round [348] log likelihood: -12916.232547
EM: Round [349] log likelihood: -12916.231261
EM: Round [350] log likelihood: -12916.229979
EM: Round [351] log likelihood: -12916.228702
EM: Round [352] log likelihood: -12916.227430
EM: Round [353] log likelihood: -12916.226162
EM: Round [354] log likelihood: -12916.224898
EM: Round [355] log likelihood: -12916.223639
EM: Round [356] log likelihood: -12916.222385
EM: Round [357] log likelihood: -12916.221135
EM: Round [358] log likelihood: -12916.219889
EM: Round [359] log likelihood: -12916.218648
EM: Round [360] log likelihood: -12916.217411
EM: Round [361] log likelihood: -12916.216178
EM: Round [362] log likelihood: -12916.214950
EM: Round [363] log likelihood: -12916.213726
EM: Round [364] log likelihood: -12916.212506
EM: Round [365] log likelihood: -12916.211290
EM: Round [366] log likelihood: -12916.210079
EM: Round [367] log likelihood: -12916.208872
EM: Round [368] log likelihood: -12916.207669
EM: Round [369] log likelihood: -12916.206471
EM: Round [370] log likelihood: -12916.205276
EM: Round [371] log likelihood: -12916.204086
EM: Round [372] log likelihood: -12916.202900
EM: Round [373] log likelihood: -12916.201718
EM: Round [374] log likelihood: -12916.200540
EM: Round [375] log likelihood: -12916.199367
EM: Round [376] log likelihood: -12916.198197
EM: Round [377] log likelihood: -12916.197031
EM: Round [378] log likelihood: -12916.195870
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EM: Round [834] log likelihood: -12915.922134
EM: Round [835] log likelihood: -12915.921865
EM: Round [836] log likelihood: -12915.921596
EM: Round [837] log likelihood: -12915.921329
EM: Round [838] log likelihood: -12915.921062
EM: Round [839] log likelihood: -12915.920796
EM: Round [840] log likelihood: -12915.920531
EM: Round [841] log likelihood: -12915.920266
EM: Round [842] log likelihood: -12915.920003
EM: Round [843] log likelihood: -12915.919740
EM: Round [844] log likelihood: -12915.919478
EM: Round [845] log likelihood: -12915.919217
EM: Round [846] log likelihood: -12915.918956
EM: Round [847] log likelihood: -12915.918697
EM: Round [848] log likelihood: -12915.918438
EM: Round [849] log likelihood: -12915.918180
EM: Round [850] log likelihood: -12915.917922
EM: Round [851] log likelihood: -12915.917666
EM: Round [852] log likelihood: -12915.917410
EM: Round [853] log likelihood: -12915.917155
EM: Round [854] log likelihood: -12915.916901
EM: Round [855] log likelihood: -12915.916648
EM: Round [856] log likelihood: -12915.916395
EM: Round [857] log likelihood: -12915.916143
EM: Round [858] log likelihood: -12915.915892
EM: Round [859] log likelihood: -12915.915642
EM: Round [860] log likelihood: -12915.915392
EM: Round [861] log likelihood: -12915.915143
EM: Round [862] log likelihood: -12915.914895
EM: Round [863] log likelihood: -12915.914648
EM: Round [864] log likelihood: -12915.914401
EM: Round [865] log likelihood: -12915.914155
EM: Round [866] log likelihood: -12915.913910
EM: Round [867] log likelihood: -12915.913666
EM: Round [868] log likelihood: -12915.913422
EM: Round [869] log likelihood: -12915.913179
EM: Round [870] log likelihood: -12915.912937
EM: Round [871] log likelihood: -12915.912695
EM: Round [872] log likelihood: -12915.912455
EM: Round [873] log likelihood: -12915.912215
EM: Round [874] log likelihood: -12915.911975
EM: Round [875] log likelihood: -12915.911737
EM: Round [876] log likelihood: -12915.911499
EM: Round [877] log likelihood: -12915.911262
EM: Round [878] log likelihood: -12915.911026
EM: Round [879] log likelihood: -12915.910790
EM: Round [880] log likelihood: -12915.910555
EM: Round [881] log likelihood: -12915.910321
EM: Round [882] log likelihood: -12915.910087
EM: Round [883] log likelihood: -12915.909854
EM: Round [884] log likelihood: -12915.909622
EM: Round [885] log likelihood: -12915.909390
EM: Round [886] log likelihood: -12915.909160
EM: Round [887] log likelihood: -12915.908930
EM: Round [888] log likelihood: -12915.908700
EM: Round [889] log likelihood: -12915.908472
EM: Round [890] log likelihood: -12915.908244
EM: Round [891] log likelihood: -12915.908016
EM: Round [892] log likelihood: -12915.907790
EM: Round [893] log likelihood: -12915.907564
EM: Round [894] log likelihood: -12915.907338
EM: Round [895] log likelihood: -12915.907114
EM: Round [896] log likelihood: -12915.906890
EM: Round [897] log likelihood: -12915.906667
EM: Round [898] log likelihood: -12915.906444
EM: Round [899] log likelihood: -12915.906222
EM: Round [900] log likelihood: -12915.906001
EM: Round [901] log likelihood: -12915.905780
EM: Round [902] log likelihood: -12915.905560
EM: Round [903] log likelihood: -12915.905341
EM: Round [904] log likelihood: -12915.905122
EM: Round [905] log likelihood: -12915.904905
EM: Round [906] log likelihood: -12915.904687
EM: Round [907] log likelihood: -12915.904471
EM: Round [908] log likelihood: -12915.904255
EM: Round [909] log likelihood: -12915.904039
EM: Round [910] log likelihood: -12915.903825
EM: Round [911] log likelihood: -12915.903611
EM: Round [912] log likelihood: -12915.903397
EM: Round [913] log likelihood: -12915.903184
EM: Round [914] log likelihood: -12915.902972
EM: Round [915] log likelihood: -12915.902761
EM: Round [916] log likelihood: -12915.902550
EM: Round [917] log likelihood: -12915.902340
EM: Round [918] log likelihood: -12915.902130
EM: Round [919] log likelihood: -12915.901921
EM: Round [920] log likelihood: -12915.901713
EM: Round [921] log likelihood: -12915.901505
EM: Round [922] log likelihood: -12915.901298
EM: Round [923] log likelihood: -12915.901091
EM: Round [924] log likelihood: -12915.900886
EM: Round [925] log likelihood: -12915.900680
EM: Round [926] log likelihood: -12915.900476
EM: Round [927] log likelihood: -12915.900272
EM: Round [928] log likelihood: -12915.900068
EM: Round [929] log likelihood: -12915.899866
EM: Round [930] log likelihood: -12915.899663
EM: Round [931] log likelihood: -12915.899462
EM: Round [932] log likelihood: -12915.899261
EM: Round [933] log likelihood: -12915.899061
EM: Round [934] log likelihood: -12915.898861
EM: Round [935] log likelihood: -12915.898662
EM: Round [936] log likelihood: -12915.898463
EM: Round [937] log likelihood: -12915.898265
EM: Round [938] log likelihood: -12915.898068
EM: Round [939] log likelihood: -12915.897871
EM: Round [940] log likelihood: -12915.897675
EM: Round [941] log likelihood: -12915.897479
EM: Round [942] log likelihood: -12915.897284
EM: Round [943] log likelihood: -12915.897090
EM: Round [944] log likelihood: -12915.896896
EM: Round [945] log likelihood: -12915.896702
EM: Round [946] log likelihood: -12915.896510
EM: Round [947] log likelihood: -12915.896318
EM: Round [948] log likelihood: -12915.896126
EM: Round [949] log likelihood: -12915.895935
EM: Round [950] log likelihood: -12915.895745
EM: Round [951] log likelihood: -12915.895555
EM: Round [952] log likelihood: -12915.895365
EM: Round [953] log likelihood: -12915.895177
EM: Round [954] log likelihood: -12915.894989
EM: Round [955] log likelihood: -12915.894801
EM: Round [956] log likelihood: -12915.894614
EM: Round [957] log likelihood: -12915.894428
EM: Round [958] log likelihood: -12915.894242
EM: Round [959] log likelihood: -12915.894056
EM: Round [960] log likelihood: -12915.893871
EM: Round [961] log likelihood: -12915.893687
EM: Round [962] log likelihood: -12915.893503
EM: Round [963] log likelihood: -12915.893320
EM: Round [964] log likelihood: -12915.893138
EM: Round [965] log likelihood: -12915.892956
EM: Round [966] log likelihood: -12915.892774
EM: Round [967] log likelihood: -12915.892593
EM: Round [968] log likelihood: -12915.892413
EM: Round [969] log likelihood: -12915.892233
EM: Round [970] log likelihood: -12915.892053
EM: Round [971] log likelihood: -12915.891875
EM: Round [972] log likelihood: -12915.891696
EM: Round [973] log likelihood: -12915.891519
EM: Round [974] log likelihood: -12915.891341
EM: Round [975] log likelihood: -12915.891165
EM: Round [976] log likelihood: -12915.890988
EM: Round [977] log likelihood: -12915.890813
EM: Round [978] log likelihood: -12915.890638
EM: Round [979] log likelihood: -12915.890463
EM: Round [980] log likelihood: -12915.890289
EM: Round [981] log likelihood: -12915.890115
EM: Round [982] log likelihood: -12915.889942
EM: Round [983] log likelihood: -12915.889770
EM: Round [984] log likelihood: -12915.889598
EM: Round [985] log likelihood: -12915.889426
EM: Round [986] log likelihood: -12915.889255
EM: Round [987] log likelihood: -12915.889085
EM: Round [988] log likelihood: -12915.888915
EM: Round [989] log likelihood: -12915.888745
EM: Round [990] log likelihood: -12915.888577
EM: Round [991] log likelihood: -12915.888408
EM: Round [992] log likelihood: -12915.888240
EM: Round [993] log likelihood: -12915.888073
EM: Round [994] log likelihood: -12915.887906
EM: Round [995] log likelihood: -12915.887739
EM: Round [996] log likelihood: -12915.887573
EM: Round [997] log likelihood: -12915.887408
EM: Round [998] log likelihood: -12915.887243
EM: Round [999] log likelihood: -12915.887078
EM: Round [1000] log likelihood: -12915.886914
EM: Round [1001] log likelihood: -12915.886751
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz: 295839766
Execution Time = 5.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa --gtf /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fa --gtf /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gtf > /tmp/nxf.UDv895oNsM/fi_workdir/microH.dat
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.UDv895oNsM/fi_workdir/microH.dat /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_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.UDv895oNsM/fi_workdir/microH.dat /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.UDv895oNsM --json_outfile /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00641_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.UDv895oNsM --json_outfile /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00641_B23MVV7LT4_1
Running: touch /tmp/nxf.UDv895oNsM/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.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00641_B23MVV7LT4_1 --html_output /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00641_B23MVV7LT4_1 --html_output /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
WARNING, no entry stored in dbm for [ENSG00000196115.13]
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 [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
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 [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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000283098.2]
WARNING, no entry stored in dbm for [ENSG00000237442.3]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.UDv895oNsM/ctat_genome_lib_build_dir > /tmp/nxf.UDv895oNsM/tih_rna_sample_00641_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.UDv895oNsM/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory