Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/d798c25ec554fab9d4789a214a8ce5/tih_rna_sample_00658_B23MVV7LT4_1.fusionreport.tsv
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/90/9025b08a00ab1a97ecc14e4d3114ab/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/fd427e0d44b8a6ccfdcb704c177af3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/9025b08a00ab1a97ecc14e4d3114ab/tih_rna_sample_00658_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/fd427e0d44b8a6ccfdcb704c177af3/.command.run
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00658_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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_00658_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/cytoBand.txt
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00658_B23MVV7LT4_1.star --out_dir /tmp/nxf.vuGnvWu9DD/fi_workdir --reads "/tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:15:48 ..... started STAR run
Jun 08 10:15:48 ..... loading genome
Jun 08 10:17:45 ... generating Suffix Array index
Jun 08 10:21:53 ... completed Suffix Array index
Jun 08 10:21:53 ..... processing annotations GTF
Jun 08 10:21:53 ..... inserting junctions into the genome indices
Jun 08 10:23:01 ..... started mapping
Jun 08 12:31:18 ..... finished mapping
Jun 08 12:31:22 ..... started sorting BAM
Jun 08 12:31:23 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 135.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00658_B23MVV7LT4_1.star --out_dir /tmp/nxf.vuGnvWu9DD/fi_workdir --reads "/tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
12:31:33 : INFO : Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1590000] -done parsing /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 4475,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 86,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'low complexity anchor region' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'seq-similar region overlap' => 68,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 52,
'excessive soft clipping' => 7667,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
' ** passed ** ' => 29722,
'small anchor length' => 90,
'num genes matched < 2' => 12,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16
};
-writing fusion junction support info.
Execution Time = 0.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[47000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[46000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[44000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[145000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[45000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[146000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[147000] -fusion SPANNING read extraction for scaff: SS18--SSX1
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[25000] -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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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[11000] -fusion SPANNING read extraction for scaff: UBE2E2--AC027229.1
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[135000] -fusion SPANNING read extraction for scaff: UBE2E2--SS18
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[11000] -fusion SPANNING read extraction for scaff: UBE2E2--RN7SL97P
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[147000] -fusion SPANNING read extraction for scaff: UBE2E2--ZNF521
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 46366,
'lacks exon overlap' => 3125
};
Execution Time = 2.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -10046.725348
EM: Round [1] log likelihood: -10045.997359
EM: Round [2] log likelihood: -10045.760535
EM: Round [3] log likelihood: -10045.523241
EM: Round [4] log likelihood: -10045.285225
EM: Round [5] log likelihood: -10045.046912
EM: Round [6] log likelihood: -10044.808894
EM: Round [7] log likelihood: -10044.571858
EM: Round [8] log likelihood: -10044.336539
EM: Round [9] log likelihood: -10044.103680
EM: Round [10] log likelihood: -10043.874001
EM: Round [11] log likelihood: -10043.648176
EM: Round [12] log likelihood: -10043.426814
EM: Round [13] log likelihood: -10043.210451
EM: Round [14] log likelihood: -10042.999546
EM: Round [15] log likelihood: -10042.794474
EM: Round [16] log likelihood: -10042.595531
EM: Round [17] log likelihood: -10042.402937
EM: Round [18] log likelihood: -10042.216838
EM: Round [19] log likelihood: -10042.037317
EM: Round [20] log likelihood: -10041.864398
EM: Round [21] log likelihood: -10041.698054
EM: Round [22] log likelihood: -10041.538214
EM: Round [23] log likelihood: -10041.384768
EM: Round [24] log likelihood: -10041.237578
EM: Round [25] log likelihood: -10041.096480
EM: Round [26] log likelihood: -10040.961290
EM: Round [27] log likelihood: -10040.831809
EM: Round [28] log likelihood: -10040.707830
EM: Round [29] log likelihood: -10040.589136
EM: Round [30] log likelihood: -10040.475510
EM: Round [31] log likelihood: -10040.366731
EM: Round [32] log likelihood: -10040.262581
EM: Round [33] log likelihood: -10040.162845
EM: Round [34] log likelihood: -10040.067310
EM: Round [35] log likelihood: -10039.975773
EM: Round [36] log likelihood: -10039.888033
EM: Round [37] log likelihood: -10039.803900
EM: Round [38] log likelihood: -10039.723188
EM: Round [39] log likelihood: -10039.645723
EM: Round [40] log likelihood: -10039.571336
EM: Round [41] log likelihood: -10039.499867
EM: Round [42] log likelihood: -10039.431163
EM: Round [43] log likelihood: -10039.365081
EM: Round [44] log likelihood: -10039.301484
EM: Round [45] log likelihood: -10039.240244
EM: Round [46] log likelihood: -10039.181238
EM: Round [47] log likelihood: -10039.124351
EM: Round [48] log likelihood: -10039.069476
EM: Round [49] log likelihood: -10039.016510
EM: Round [50] log likelihood: -10038.965358
EM: Round [51] log likelihood: -10038.915929
EM: Round [52] log likelihood: -10038.868139
EM: Round [53] log likelihood: -10038.821908
EM: Round [54] log likelihood: -10038.777160
EM: Round [55] log likelihood: -10038.733825
EM: Round [56] log likelihood: -10038.691837
EM: Round [57] log likelihood: -10038.651133
EM: Round [58] log likelihood: -10038.611655
EM: Round [59] log likelihood: -10038.573347
EM: Round [60] log likelihood: -10038.536157
EM: Round [61] log likelihood: -10038.500037
EM: Round [62] log likelihood: -10038.464940
EM: Round [63] log likelihood: -10038.430823
EM: Round [64] log likelihood: -10038.397644
EM: Round [65] log likelihood: -10038.365365
EM: Round [66] log likelihood: -10038.333950
EM: Round [67] log likelihood: -10038.303363
EM: Round [68] log likelihood: -10038.273572
EM: Round [69] log likelihood: -10038.244546
EM: Round [70] log likelihood: -10038.216256
EM: Round [71] log likelihood: -10038.188674
EM: Round [72] log likelihood: -10038.161773
EM: Round [73] log likelihood: -10038.135529
EM: Round [74] log likelihood: -10038.109918
EM: Round [75] log likelihood: -10038.084917
EM: Round [76] log likelihood: -10038.060504
EM: Round [77] log likelihood: -10038.036660
EM: Round [78] log likelihood: -10038.013364
EM: Round [79] log likelihood: -10037.990599
EM: Round [80] log likelihood: -10037.968346
EM: Round [81] log likelihood: -10037.946588
EM: Round [82] log likelihood: -10037.925310
EM: Round [83] log likelihood: -10037.904496
EM: Round [84] log likelihood: -10037.884130
EM: Round [85] log likelihood: -10037.864199
EM: Round [86] log likelihood: -10037.844690
EM: Round [87] log likelihood: -10037.825589
EM: Round [88] log likelihood: -10037.806883
EM: Round [89] log likelihood: -10037.788562
EM: Round [90] log likelihood: -10037.770612
EM: Round [91] log likelihood: -10037.753024
EM: Round [92] log likelihood: -10037.735786
EM: Round [93] log likelihood: -10037.718889
EM: Round [94] log likelihood: -10037.702322
EM: Round [95] log likelihood: -10037.686076
EM: Round [96] log likelihood: -10037.670142
EM: Round [97] log likelihood: -10037.654510
EM: Round [98] log likelihood: -10037.639174
EM: Round [99] log likelihood: -10037.624124
EM: Round [100] log likelihood: -10037.609352
EM: Round [101] log likelihood: -10037.594851
EM: Round [102] log likelihood: -10037.580614
EM: Round [103] log likelihood: -10037.566633
EM: Round [104] log likelihood: -10037.552902
EM: Round [105] log likelihood: -10037.539413
EM: Round [106] log likelihood: -10037.526161
EM: Round [107] log likelihood: -10037.513139
EM: Round [108] log likelihood: -10037.500342
EM: Round [109] log likelihood: -10037.487762
EM: Round [110] log likelihood: -10037.475396
EM: Round [111] log likelihood: -10037.463237
EM: Round [112] log likelihood: -10037.451279
EM: Round [113] log likelihood: -10037.439519
EM: Round [114] log likelihood: -10037.427951
EM: Round [115] log likelihood: -10037.416569
EM: Round [116] log likelihood: -10037.405371
EM: Round [117] log likelihood: -10037.394350
EM: Round [118] log likelihood: -10037.383502
EM: Round [119] log likelihood: -10037.372824
EM: Round [120] log likelihood: -10037.362311
EM: Round [121] log likelihood: -10037.351959
EM: Round [122] log likelihood: -10037.341765
EM: Round [123] log likelihood: -10037.331724
EM: Round [124] log likelihood: -10037.321832
EM: Round [125] log likelihood: -10037.312087
EM: Round [126] log likelihood: -10037.302485
EM: Round [127] log likelihood: -10037.293022
EM: Round [128] log likelihood: -10037.283695
EM: Round [129] log likelihood: -10037.274501
EM: Round [130] log likelihood: -10037.265437
EM: Round [131] log likelihood: -10037.256500
EM: Round [132] log likelihood: -10037.247687
EM: Round [133] log likelihood: -10037.238995
EM: Round [134] log likelihood: -10037.230422
EM: Round [135] log likelihood: -10037.221964
EM: Round [136] log likelihood: -10037.213619
EM: Round [137] log likelihood: -10037.205384
EM: Round [138] log likelihood: -10037.197258
EM: Round [139] log likelihood: -10037.189238
EM: Round [140] log likelihood: -10037.181320
EM: Round [141] log likelihood: -10037.173504
EM: Round [142] log likelihood: -10037.165787
EM: Round [143] log likelihood: -10037.158166
EM: Round [144] log likelihood: -10037.150640
EM: Round [145] log likelihood: -10037.143207
EM: Round [146] log likelihood: -10037.135864
EM: Round [147] log likelihood: -10037.128609
EM: Round [148] log likelihood: -10037.121442
EM: Round [149] log likelihood: -10037.114359
EM: Round [150] log likelihood: -10037.107359
EM: Round [151] log likelihood: -10037.100441
EM: Round [152] log likelihood: -10037.093603
EM: Round [153] log likelihood: -10037.086842
EM: Round [154] log likelihood: -10037.080158
EM: Round [155] log likelihood: -10037.073549
EM: Round [156] log likelihood: -10037.067013
EM: Round [157] log likelihood: -10037.060549
EM: Round [158] log likelihood: -10037.054155
EM: Round [159] log likelihood: -10037.047830
EM: Round [160] log likelihood: -10037.041573
EM: Round [161] log likelihood: -10037.035382
EM: Round [162] log likelihood: -10037.029256
EM: Round [163] log likelihood: -10037.023193
EM: Round [164] log likelihood: -10037.017193
EM: Round [165] log likelihood: -10037.011254
EM: Round [166] log likelihood: -10037.005375
EM: Round [167] log likelihood: -10036.999555
EM: Round [168] log likelihood: -10036.993793
EM: Round [169] log likelihood: -10036.988087
EM: Round [170] log likelihood: -10036.982437
EM: Round [171] log likelihood: -10036.976841
EM: Round [172] log likelihood: -10036.971298
EM: Round [173] log likelihood: -10036.965808
EM: Round [174] log likelihood: -10036.960370
EM: Round [175] log likelihood: -10036.954982
EM: Round [176] log likelihood: -10036.949643
EM: Round [177] log likelihood: -10036.944353
EM: Round [178] log likelihood: -10036.939111
EM: Round [179] log likelihood: -10036.933916
EM: Round [180] log likelihood: -10036.928768
EM: Round [181] log likelihood: -10036.923664
EM: Round [182] log likelihood: -10036.918605
EM: Round [183] log likelihood: -10036.913589
EM: Round [184] log likelihood: -10036.908617
EM: Round [185] log likelihood: -10036.903686
EM: Round [186] log likelihood: -10036.898797
EM: Round [187] log likelihood: -10036.893949
EM: Round [188] log likelihood: -10036.889141
EM: Round [189] log likelihood: -10036.884372
EM: Round [190] log likelihood: -10036.879642
EM: Round [191] log likelihood: -10036.874950
EM: Round [192] log likelihood: -10036.870296
EM: Round [193] log likelihood: -10036.865678
EM: Round [194] log likelihood: -10036.861096
EM: Round [195] log likelihood: -10036.856550
EM: Round [196] log likelihood: -10036.852039
EM: Round [197] log likelihood: -10036.847563
EM: Round [198] log likelihood: -10036.843120
EM: Round [199] log likelihood: -10036.838711
EM: Round [200] log likelihood: -10036.834334
EM: Round [201] log likelihood: -10036.829990
EM: Round [202] log likelihood: -10036.825678
EM: Round [203] log likelihood: -10036.821397
EM: Round [204] log likelihood: -10036.817147
EM: Round [205] log likelihood: -10036.812927
EM: Round [206] log likelihood: -10036.808738
EM: Round [207] log likelihood: -10036.804577
EM: Round [208] log likelihood: -10036.800446
EM: Round [209] log likelihood: -10036.796343
EM: Round [210] log likelihood: -10036.792269
EM: Round [211] log likelihood: -10036.788222
EM: Round [212] log likelihood: -10036.784203
EM: Round [213] log likelihood: -10036.780210
EM: Round [214] log likelihood: -10036.776244
EM: Round [215] log likelihood: -10036.772305
EM: Round [216] log likelihood: -10036.768391
EM: Round [217] log likelihood: -10036.764502
EM: Round [218] log likelihood: -10036.760639
EM: Round [219] log likelihood: -10036.756801
EM: Round [220] log likelihood: -10036.752987
EM: Round [221] log likelihood: -10036.749197
EM: Round [222] log likelihood: -10036.745430
EM: Round [223] log likelihood: -10036.741688
EM: Round [224] log likelihood: -10036.737968
EM: Round [225] log likelihood: -10036.734271
EM: Round [226] log likelihood: -10036.730597
EM: Round [227] log likelihood: -10036.726945
EM: Round [228] log likelihood: -10036.723315
EM: Round [229] log likelihood: -10036.719707
EM: Round [230] log likelihood: -10036.716120
EM: Round [231] log likelihood: -10036.712554
EM: Round [232] log likelihood: -10036.709009
EM: Round [233] log likelihood: -10036.705485
EM: Round [234] log likelihood: -10036.701981
EM: Round [235] log likelihood: -10036.698497
EM: Round [236] log likelihood: -10036.695033
EM: Round [237] log likelihood: -10036.691589
EM: Round [238] log likelihood: -10036.688164
EM: Round [239] log likelihood: -10036.684758
EM: Round [240] log likelihood: -10036.681371
EM: Round [241] log likelihood: -10036.678003
EM: Round [242] log likelihood: -10036.674654
EM: Round [243] log likelihood: -10036.671322
EM: Round [244] log likelihood: -10036.668009
EM: Round [245] log likelihood: -10036.664714
EM: Round [246] log likelihood: -10036.661436
EM: Round [247] log likelihood: -10036.658176
EM: Round [248] log likelihood: -10036.654933
EM: Round [249] log likelihood: -10036.651707
EM: Round [250] log likelihood: -10036.648498
EM: Round [251] log likelihood: -10036.645306
EM: Round [252] log likelihood: -10036.642131
EM: Round [253] log likelihood: -10036.638972
EM: Round [254] log likelihood: -10036.635829
EM: Round [255] log likelihood: -10036.632702
EM: Round [256] log likelihood: -10036.629591
EM: Round [257] log likelihood: -10036.626495
EM: Round [258] log likelihood: -10036.623415
EM: Round [259] log likelihood: -10036.620351
EM: Round [260] log likelihood: -10036.617302
EM: Round [261] log likelihood: -10036.614268
EM: Round [262] log likelihood: -10036.611249
EM: Round [263] log likelihood: -10036.608244
EM: Round [264] log likelihood: -10036.605255
EM: Round [265] log likelihood: -10036.602280
EM: Round [266] log likelihood: -10036.599319
EM: Round [267] log likelihood: -10036.596372
EM: Round [268] log likelihood: -10036.593440
EM: Round [269] log likelihood: -10036.590521
EM: Round [270] log likelihood: -10036.587617
EM: Round [271] log likelihood: -10036.584726
EM: Round [272] log likelihood: -10036.581849
EM: Round [273] log likelihood: -10036.578985
EM: Round [274] log likelihood: -10036.576134
EM: Round [275] log likelihood: -10036.573297
EM: Round [276] log likelihood: -10036.570473
EM: Round [277] log likelihood: -10036.567662
EM: Round [278] log likelihood: -10036.564863
EM: Round [279] log likelihood: -10036.562078
EM: Round [280] log likelihood: -10036.559305
EM: Round [281] log likelihood: -10036.556545
EM: Round [282] log likelihood: -10036.553797
EM: Round [283] log likelihood: -10036.551062
EM: Round [284] log likelihood: -10036.548338
EM: Round [285] log likelihood: -10036.545627
EM: Round [286] log likelihood: -10036.542928
EM: Round [287] log likelihood: -10036.540241
EM: Round [288] log likelihood: -10036.537566
EM: Round [289] log likelihood: -10036.534903
EM: Round [290] log likelihood: -10036.532251
EM: Round [291] log likelihood: -10036.529611
EM: Round [292] log likelihood: -10036.526982
EM: Round [293] log likelihood: -10036.524364
EM: Round [294] log likelihood: -10036.521758
EM: Round [295] log likelihood: -10036.519163
EM: Round [296] log likelihood: -10036.516580
EM: Round [297] log likelihood: -10036.514007
EM: Round [298] log likelihood: -10036.511445
EM: Round [299] log likelihood: -10036.508895
EM: Round [300] log likelihood: -10036.506354
EM: Round [301] log likelihood: -10036.503825
EM: Round [302] log likelihood: -10036.501306
EM: Round [303] log likelihood: -10036.498798
EM: Round [304] log likelihood: -10036.496301
EM: Round [305] log likelihood: -10036.493813
EM: Round [306] log likelihood: -10036.491337
EM: Round [307] log likelihood: -10036.488870
EM: Round [308] log likelihood: -10036.486414
EM: Round [309] log likelihood: -10036.483967
EM: Round [310] log likelihood: -10036.481531
EM: Round [311] log likelihood: -10036.479105
EM: Round [312] log likelihood: -10036.476688
EM: Round [313] log likelihood: -10036.474282
EM: Round [314] log likelihood: -10036.471885
EM: Round [315] log likelihood: -10036.469498
EM: Round [316] log likelihood: -10036.467121
EM: Round [317] log likelihood: -10036.464753
EM: Round [318] log likelihood: -10036.462395
EM: Round [319] log likelihood: -10036.460046
EM: Round [320] log likelihood: -10036.457706
EM: Round [321] log likelihood: -10036.455376
EM: Round [322] log likelihood: -10036.453056
EM: Round [323] log likelihood: -10036.450744
EM: Round [324] log likelihood: -10036.448442
EM: Round [325] log likelihood: -10036.446148
EM: Round [326] log likelihood: -10036.443864
EM: Round [327] log likelihood: -10036.441589
EM: Round [328] log likelihood: -10036.439322
EM: Round [329] log likelihood: -10036.437065
EM: Round [330] log likelihood: -10036.434816
EM: Round [331] log likelihood: -10036.432576
EM: Round [332] log likelihood: -10036.430345
EM: Round [333] log likelihood: -10036.428122
EM: Round [334] log likelihood: -10036.425909
EM: Round [335] log likelihood: -10036.423703
EM: Round [336] log likelihood: -10036.421506
EM: Round [337] log likelihood: -10036.419318
EM: Round [338] log likelihood: -10036.417138
EM: Round [339] log likelihood: -10036.414966
EM: Round [340] log likelihood: -10036.412803
EM: Round [341] log likelihood: -10036.410648
EM: Round [342] log likelihood: -10036.408501
EM: Round [343] log likelihood: -10036.406362
EM: Round [344] log likelihood: -10036.404231
EM: Round [345] log likelihood: -10036.402109
EM: Round [346] log likelihood: -10036.399994
EM: Round [347] log likelihood: -10036.397888
EM: Round [348] log likelihood: -10036.395789
EM: Round [349] log likelihood: -10036.393698
EM: Round [350] log likelihood: -10036.391615
EM: Round [351] log likelihood: -10036.389540
EM: Round [352] log likelihood: -10036.387473
EM: Round [353] log likelihood: -10036.385413
EM: Round [354] log likelihood: -10036.383361
EM: Round [355] log likelihood: -10036.381317
EM: Round [356] log likelihood: -10036.379280
EM: Round [357] log likelihood: -10036.377251
EM: Round [358] log likelihood: -10036.375229
EM: Round [359] log likelihood: -10036.373215
EM: Round [360] log likelihood: -10036.371208
EM: Round [361] log likelihood: -10036.369209
EM: Round [362] log likelihood: -10036.367217
EM: Round [363] log likelihood: -10036.365232
EM: Round [364] log likelihood: -10036.363254
EM: Round [365] log likelihood: -10036.361284
EM: Round [366] log likelihood: -10036.359321
EM: Round [367] log likelihood: -10036.357365
EM: Round [368] log likelihood: -10036.355416
EM: Round [369] log likelihood: -10036.353474
EM: Round [370] log likelihood: -10036.351540
EM: Round [371] log likelihood: -10036.349612
EM: Round [372] log likelihood: -10036.347691
EM: Round [373] log likelihood: -10036.345778
EM: Round [374] log likelihood: -10036.343871
EM: Round [375] log likelihood: -10036.341971
EM: Round [376] log likelihood: -10036.340078
EM: Round [377] log likelihood: -10036.338191
EM: Round [378] log likelihood: -10036.336312
EM: Round [379] log likelihood: -10036.334439
EM: Round [380] log likelihood: -10036.332573
EM: Round [381] log likelihood: -10036.330713
EM: Round [382] log likelihood: -10036.328860
EM: Round [383] log likelihood: -10036.327014
EM: Round [384] log likelihood: -10036.325174
EM: Round [385] log likelihood: -10036.323341
EM: Round [386] log likelihood: -10036.321514
EM: Round [387] log likelihood: -10036.319694
EM: Round [388] log likelihood: -10036.317880
EM: Round [389] log likelihood: -10036.316073
EM: Round [390] log likelihood: -10036.314272
EM: Round [391] log likelihood: -10036.312478
EM: Round [392] log likelihood: -10036.310689
EM: Round [393] log likelihood: -10036.308907
EM: Round [394] log likelihood: -10036.307131
EM: Round [395] log likelihood: -10036.305362
EM: Round [396] log likelihood: -10036.303599
EM: Round [397] log likelihood: -10036.301841
EM: Round [398] log likelihood: -10036.300090
EM: Round [399] log likelihood: -10036.298346
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EM: Round [859] log likelihood: -10035.876590
EM: Round [860] log likelihood: -10035.876157
EM: Round [861] log likelihood: -10035.875726
EM: Round [862] log likelihood: -10035.875295
EM: Round [863] log likelihood: -10035.874866
EM: Round [864] log likelihood: -10035.874438
EM: Round [865] log likelihood: -10035.874011
EM: Round [866] log likelihood: -10035.873586
EM: Round [867] log likelihood: -10035.873161
EM: Round [868] log likelihood: -10035.872738
EM: Round [869] log likelihood: -10035.872315
EM: Round [870] log likelihood: -10035.871894
EM: Round [871] log likelihood: -10035.871475
EM: Round [872] log likelihood: -10035.871056
EM: Round [873] log likelihood: -10035.870638
EM: Round [874] log likelihood: -10035.870222
EM: Round [875] log likelihood: -10035.869807
EM: Round [876] log likelihood: -10035.869393
EM: Round [877] log likelihood: -10035.868980
EM: Round [878] log likelihood: -10035.868568
EM: Round [879] log likelihood: -10035.868157
EM: Round [880] log likelihood: -10035.867748
EM: Round [881] log likelihood: -10035.867339
EM: Round [882] log likelihood: -10035.866932
EM: Round [883] log likelihood: -10035.866526
EM: Round [884] log likelihood: -10035.866121
EM: Round [885] log likelihood: -10035.865717
EM: Round [886] log likelihood: -10035.865314
EM: Round [887] log likelihood: -10035.864912
EM: Round [888] log likelihood: -10035.864512
EM: Round [889] log likelihood: -10035.864112
EM: Round [890] log likelihood: -10035.863714
EM: Round [891] log likelihood: -10035.863316
EM: Round [892] log likelihood: -10035.862920
EM: Round [893] log likelihood: -10035.862525
EM: Round [894] log likelihood: -10035.862131
EM: Round [895] log likelihood: -10035.861738
EM: Round [896] log likelihood: -10035.861346
EM: Round [897] log likelihood: -10035.860955
EM: Round [898] log likelihood: -10035.860566
EM: Round [899] log likelihood: -10035.860177
EM: Round [900] log likelihood: -10035.859789
EM: Round [901] log likelihood: -10035.859403
EM: Round [902] log likelihood: -10035.859017
EM: Round [903] log likelihood: -10035.858633
EM: Round [904] log likelihood: -10035.858249
EM: Round [905] log likelihood: -10035.857867
EM: Round [906] log likelihood: -10035.857486
EM: Round [907] log likelihood: -10035.857106
EM: Round [908] log likelihood: -10035.856726
EM: Round [909] log likelihood: -10035.856348
EM: Round [910] log likelihood: -10035.855971
EM: Round [911] log likelihood: -10035.855595
EM: Round [912] log likelihood: -10035.855220
EM: Round [913] log likelihood: -10035.854846
EM: Round [914] log likelihood: -10035.854473
EM: Round [915] log likelihood: -10035.854101
EM: Round [916] log likelihood: -10035.853730
EM: Round [917] log likelihood: -10035.853360
EM: Round [918] log likelihood: -10035.852991
EM: Round [919] log likelihood: -10035.852623
EM: Round [920] log likelihood: -10035.852256
EM: Round [921] log likelihood: -10035.851890
EM: Round [922] log likelihood: -10035.851525
EM: Round [923] log likelihood: -10035.851161
EM: Round [924] log likelihood: -10035.850798
EM: Round [925] log likelihood: -10035.850436
EM: Round [926] log likelihood: -10035.850075
EM: Round [927] log likelihood: -10035.849715
EM: Round [928] log likelihood: -10035.849356
EM: Round [929] log likelihood: -10035.848998
EM: Round [930] log likelihood: -10035.848641
EM: Round [931] log likelihood: -10035.848285
EM: Round [932] log likelihood: -10035.847930
EM: Round [933] log likelihood: -10035.847576
EM: Round [934] log likelihood: -10035.847223
EM: Round [935] log likelihood: -10035.846871
EM: Round [936] log likelihood: -10035.846519
EM: Round [937] log likelihood: -10035.846169
EM: Round [938] log likelihood: -10035.845820
EM: Round [939] log likelihood: -10035.845471
EM: Round [940] log likelihood: -10035.845124
EM: Round [941] log likelihood: -10035.844778
EM: Round [942] log likelihood: -10035.844432
EM: Round [943] log likelihood: -10035.844087
EM: Round [944] log likelihood: -10035.843744
EM: Round [945] log likelihood: -10035.843401
EM: Round [946] log likelihood: -10035.843059
EM: Round [947] log likelihood: -10035.842718
EM: Round [948] log likelihood: -10035.842378
EM: Round [949] log likelihood: -10035.842039
EM: Round [950] log likelihood: -10035.841701
EM: Round [951] log likelihood: -10035.841364
EM: Round [952] log likelihood: -10035.841028
EM: Round [953] log likelihood: -10035.840692
EM: Round [954] log likelihood: -10035.840358
EM: Round [955] log likelihood: -10035.840024
EM: Round [956] log likelihood: -10035.839692
EM: Round [957] log likelihood: -10035.839360
EM: Round [958] log likelihood: -10035.839029
EM: Round [959] log likelihood: -10035.838699
EM: Round [960] log likelihood: -10035.838370
EM: Round [961] log likelihood: -10035.838042
EM: Round [962] log likelihood: -10035.837715
EM: Round [963] log likelihood: -10035.837389
EM: Round [964] log likelihood: -10035.837063
EM: Round [965] log likelihood: -10035.836738
EM: Round [966] log likelihood: -10035.836415
EM: Round [967] log likelihood: -10035.836092
EM: Round [968] log likelihood: -10035.835770
EM: Round [969] log likelihood: -10035.835449
EM: Round [970] log likelihood: -10035.835129
EM: Round [971] log likelihood: -10035.834809
EM: Round [972] log likelihood: -10035.834491
EM: Round [973] log likelihood: -10035.834173
EM: Round [974] log likelihood: -10035.833856
EM: Round [975] log likelihood: -10035.833540
EM: Round [976] log likelihood: -10035.833225
EM: Round [977] log likelihood: -10035.832911
EM: Round [978] log likelihood: -10035.832598
EM: Round [979] log likelihood: -10035.832285
EM: Round [980] log likelihood: -10035.831974
EM: Round [981] log likelihood: -10035.831663
EM: Round [982] log likelihood: -10035.831353
EM: Round [983] log likelihood: -10035.831044
EM: Round [984] log likelihood: -10035.830735
EM: Round [985] log likelihood: -10035.830428
EM: Round [986] log likelihood: -10035.830121
EM: Round [987] log likelihood: -10035.829815
EM: Round [988] log likelihood: -10035.829510
EM: Round [989] log likelihood: -10035.829206
EM: Round [990] log likelihood: -10035.828903
EM: Round [991] log likelihood: -10035.828600
EM: Round [992] log likelihood: -10035.828299
EM: Round [993] log likelihood: -10035.827998
EM: Round [994] log likelihood: -10035.827698
EM: Round [995] log likelihood: -10035.827398
EM: Round [996] log likelihood: -10035.827100
EM: Round [997] log likelihood: -10035.826802
EM: Round [998] log likelihood: -10035.826505
EM: Round [999] log likelihood: -10035.826209
EM: Round [1000] log likelihood: -10035.825914
EM: Round [1001] log likelihood: -10035.825620
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/tih_rna_sample_00658_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa > /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir
-done, see /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7640.985514
EM: Round [1] log likelihood: -7640.775431
EM: Round [2] log likelihood: -7640.760313
EM: Round [3] log likelihood: -7640.745555
EM: Round [4] log likelihood: -7640.730942
EM: Round [5] log likelihood: -7640.716472
EM: Round [6] log likelihood: -7640.702142
EM: Round [7] log likelihood: -7640.687951
EM: Round [8] log likelihood: -7640.673895
EM: Round [9] log likelihood: -7640.659973
EM: Round [10] log likelihood: -7640.646182
EM: Round [11] log likelihood: -7640.632520
EM: Round [12] log likelihood: -7640.618985
EM: Round [13] log likelihood: -7640.605575
EM: Round [14] log likelihood: -7640.592288
EM: Round [15] log likelihood: -7640.579123
EM: Round [16] log likelihood: -7640.566077
EM: Round [17] log likelihood: -7640.553148
EM: Round [18] log likelihood: -7640.540335
EM: Round [19] log likelihood: -7640.527636
EM: Round [20] log likelihood: -7640.515048
EM: Round [21] log likelihood: -7640.502572
EM: Round [22] log likelihood: -7640.490204
EM: Round [23] log likelihood: -7640.477943
EM: Round [24] log likelihood: -7640.465788
EM: Round [25] log likelihood: -7640.453737
EM: Round [26] log likelihood: -7640.441789
EM: Round [27] log likelihood: -7640.429941
EM: Round [28] log likelihood: -7640.418194
EM: Round [29] log likelihood: -7640.406544
EM: Round [30] log likelihood: -7640.394991
EM: Round [31] log likelihood: -7640.383534
EM: Round [32] log likelihood: -7640.372171
EM: Round [33] log likelihood: -7640.360901
EM: Round [34] log likelihood: -7640.349723
EM: Round [35] log likelihood: -7640.338635
EM: Round [36] log likelihood: -7640.327635
EM: Round [37] log likelihood: -7640.316724
EM: Round [38] log likelihood: -7640.305900
EM: Round [39] log likelihood: -7640.295161
EM: Round [40] log likelihood: -7640.284507
EM: Round [41] log likelihood: -7640.273936
EM: Round [42] log likelihood: -7640.263447
EM: Round [43] log likelihood: -7640.253040
EM: Round [44] log likelihood: -7640.242712
EM: Round [45] log likelihood: -7640.232464
EM: Round [46] log likelihood: -7640.222294
EM: Round [47] log likelihood: -7640.212201
EM: Round [48] log likelihood: -7640.202184
EM: Round [49] log likelihood: -7640.192242
EM: Round [50] log likelihood: -7640.182375
EM: Round [51] log likelihood: -7640.172581
EM: Round [52] log likelihood: -7640.162860
EM: Round [53] log likelihood: -7640.153210
EM: Round [54] log likelihood: -7640.143631
EM: Round [55] log likelihood: -7640.134121
EM: Round [56] log likelihood: -7640.124681
EM: Round [57] log likelihood: -7640.115309
EM: Round [58] log likelihood: -7640.106004
EM: Round [59] log likelihood: -7640.096766
EM: Round [60] log likelihood: -7640.087594
EM: Round [61] log likelihood: -7640.078487
EM: Round [62] log likelihood: -7640.069444
EM: Round [63] log likelihood: -7640.060464
EM: Round [64] log likelihood: -7640.051548
EM: Round [65] log likelihood: -7640.042693
EM: Round [66] log likelihood: -7640.033900
EM: Round [67] log likelihood: -7640.025168
EM: Round [68] log likelihood: -7640.016496
EM: Round [69] log likelihood: -7640.007883
EM: Round [70] log likelihood: -7639.999329
EM: Round [71] log likelihood: -7639.990832
EM: Round [72] log likelihood: -7639.982394
EM: Round [73] log likelihood: -7639.974012
EM: Round [74] log likelihood: -7639.965686
EM: Round [75] log likelihood: -7639.957416
EM: Round [76] log likelihood: -7639.949201
EM: Round [77] log likelihood: -7639.941040
EM: Round [78] log likelihood: -7639.932933
EM: Round [79] log likelihood: -7639.924879
EM: Round [80] log likelihood: -7639.916878
EM: Round [81] log likelihood: -7639.908929
EM: Round [82] log likelihood: -7639.901032
EM: Round [83] log likelihood: -7639.893185
EM: Round [84] log likelihood: -7639.885389
EM: Round [85] log likelihood: -7639.877643
EM: Round [86] log likelihood: -7639.869947
EM: Round [87] log likelihood: -7639.862300
EM: Round [88] log likelihood: -7639.854701
EM: Round [89] log likelihood: -7639.847150
EM: Round [90] log likelihood: -7639.839646
EM: Round [91] log likelihood: -7639.832190
EM: Round [92] log likelihood: -7639.824780
EM: Round [93] log likelihood: -7639.817416
EM: Round [94] log likelihood: -7639.810098
EM: Round [95] log likelihood: -7639.802825
EM: Round [96] log likelihood: -7639.795597
EM: Round [97] log likelihood: -7639.788413
EM: Round [98] log likelihood: -7639.781273
EM: Round [99] log likelihood: -7639.774177
EM: Round [100] log likelihood: -7639.767124
EM: Round [101] log likelihood: -7639.760113
EM: Round [102] log likelihood: -7639.753144
EM: Round [103] log likelihood: -7639.746218
EM: Round [104] log likelihood: -7639.739332
EM: Round [105] log likelihood: -7639.732488
EM: Round [106] log likelihood: -7639.725685
EM: Round [107] log likelihood: -7639.718921
EM: Round [108] log likelihood: -7639.712198
EM: Round [109] log likelihood: -7639.705514
EM: Round [110] log likelihood: -7639.698870
EM: Round [111] log likelihood: -7639.692264
EM: Round [112] log likelihood: -7639.685697
EM: Round [113] log likelihood: -7639.679167
EM: Round [114] log likelihood: -7639.672676
EM: Round [115] log likelihood: -7639.666222
EM: Round [116] log likelihood: -7639.659805
EM: Round [117] log likelihood: -7639.653425
EM: Round [118] log likelihood: -7639.647081
EM: Round [119] log likelihood: -7639.640774
EM: Round [120] log likelihood: -7639.634502
EM: Round [121] log likelihood: -7639.628266
EM: Round [122] log likelihood: -7639.622065
EM: Round [123] log likelihood: -7639.615899
EM: Round [124] log likelihood: -7639.609767
EM: Round [125] log likelihood: -7639.603670
EM: Round [126] log likelihood: -7639.597607
EM: Round [127] log likelihood: -7639.591577
EM: Round [128] log likelihood: -7639.585581
EM: Round [129] log likelihood: -7639.579617
EM: Round [130] log likelihood: -7639.573687
EM: Round [131] log likelihood: -7639.567789
EM: Round [132] log likelihood: -7639.561924
EM: Round [133] log likelihood: -7639.556090
EM: Round [134] log likelihood: -7639.550289
EM: Round [135] log likelihood: -7639.544518
EM: Round [136] log likelihood: -7639.538779
EM: Round [137] log likelihood: -7639.533071
EM: Round [138] log likelihood: -7639.527394
EM: Round [139] log likelihood: -7639.521747
EM: Round [140] log likelihood: -7639.516130
EM: Round [141] log likelihood: -7639.510544
EM: Round [142] log likelihood: -7639.504987
EM: Round [143] log likelihood: -7639.499459
EM: Round [144] log likelihood: -7639.493961
EM: Round [145] log likelihood: -7639.488491
EM: Round [146] log likelihood: -7639.483051
EM: Round [147] log likelihood: -7639.477639
EM: Round [148] log likelihood: -7639.472255
EM: Round [149] log likelihood: -7639.466900
EM: Round [150] log likelihood: -7639.461572
EM: Round [151] log likelihood: -7639.456272
EM: Round [152] log likelihood: -7639.451000
EM: Round [153] log likelihood: -7639.445754
EM: Round [154] log likelihood: -7639.440536
EM: Round [155] log likelihood: -7639.435344
EM: Round [156] log likelihood: -7639.430179
EM: Round [157] log likelihood: -7639.425041
EM: Round [158] log likelihood: -7639.419929
EM: Round [159] log likelihood: -7639.414842
EM: Round [160] log likelihood: -7639.409782
EM: Round [161] log likelihood: -7639.404747
EM: Round [162] log likelihood: -7639.399737
EM: Round [163] log likelihood: -7639.394753
EM: Round [164] log likelihood: -7639.389793
EM: Round [165] log likelihood: -7639.384859
EM: Round [166] log likelihood: -7639.379949
EM: Round [167] log likelihood: -7639.375064
EM: Round [168] log likelihood: -7639.370203
EM: Round [169] log likelihood: -7639.365366
EM: Round [170] log likelihood: -7639.360553
EM: Round [171] log likelihood: -7639.355764
EM: Round [172] log likelihood: -7639.350998
EM: Round [173] log likelihood: -7639.346256
EM: Round [174] log likelihood: -7639.341537
EM: Round [175] log likelihood: -7639.336841
EM: Round [176] log likelihood: -7639.332168
EM: Round [177] log likelihood: -7639.327517
EM: Round [178] log likelihood: -7639.322890
EM: Round [179] log likelihood: -7639.318284
EM: Round [180] log likelihood: -7639.313701
EM: Round [181] log likelihood: -7639.309141
EM: Round [182] log likelihood: -7639.304602
EM: Round [183] log likelihood: -7639.300084
EM: Round [184] log likelihood: -7639.295589
EM: Round [185] log likelihood: -7639.291115
EM: Round [186] log likelihood: -7639.286662
EM: Round [187] log likelihood: -7639.282230
EM: Round [188] log likelihood: -7639.277820
EM: Round [189] log likelihood: -7639.273430
EM: Round [190] log likelihood: -7639.269061
EM: Round [191] log likelihood: -7639.264713
EM: Round [192] log likelihood: -7639.260385
EM: Round [193] log likelihood: -7639.256078
EM: Round [194] log likelihood: -7639.251790
EM: Round [195] log likelihood: -7639.247523
EM: Round [196] log likelihood: -7639.243276
EM: Round [197] log likelihood: -7639.239048
EM: Round [198] log likelihood: -7639.234840
EM: Round [199] log likelihood: -7639.230652
EM: Round [200] log likelihood: -7639.226483
EM: Round [201] log likelihood: -7639.222333
EM: Round [202] log likelihood: -7639.218202
EM: Round [203] log likelihood: -7639.214090
EM: Round [204] log likelihood: -7639.209998
EM: Round [205] log likelihood: -7639.205924
EM: Round [206] log likelihood: -7639.201868
EM: Round [207] log likelihood: -7639.197831
EM: Round [208] log likelihood: -7639.193812
EM: Round [209] log likelihood: -7639.189812
EM: Round [210] log likelihood: -7639.185830
EM: Round [211] log likelihood: -7639.181866
EM: Round [212] log likelihood: -7639.177919
EM: Round [213] log likelihood: -7639.173991
EM: Round [214] log likelihood: -7639.170080
EM: Round [215] log likelihood: -7639.166187
EM: Round [216] log likelihood: -7639.162311
EM: Round [217] log likelihood: -7639.158452
EM: Round [218] log likelihood: -7639.154611
EM: Round [219] log likelihood: -7639.150787
EM: Round [220] log likelihood: -7639.146980
EM: Round [221] log likelihood: -7639.143189
EM: Round [222] log likelihood: -7639.139416
EM: Round [223] log likelihood: -7639.135659
EM: Round [224] log likelihood: -7639.131919
EM: Round [225] log likelihood: -7639.128195
EM: Round [226] log likelihood: -7639.124487
EM: Round [227] log likelihood: -7639.120796
EM: Round [228] log likelihood: -7639.117121
EM: Round [229] log likelihood: -7639.113462
EM: Round [230] log likelihood: -7639.109819
EM: Round [231] log likelihood: -7639.106192
EM: Round [232] log likelihood: -7639.102581
EM: Round [233] log likelihood: -7639.098985
EM: Round [234] log likelihood: -7639.095405
EM: Round [235] log likelihood: -7639.091841
EM: Round [236] log likelihood: -7639.088291
EM: Round [237] log likelihood: -7639.084758
EM: Round [238] log likelihood: -7639.081239
EM: Round [239] log likelihood: -7639.077735
EM: Round [240] log likelihood: -7639.074247
EM: Round [241] log likelihood: -7639.070773
EM: Round [242] log likelihood: -7639.067314
EM: Round [243] log likelihood: -7639.063870
EM: Round [244] log likelihood: -7639.060441
EM: Round [245] log likelihood: -7639.057026
EM: Round [246] log likelihood: -7639.053626
EM: Round [247] log likelihood: -7639.050240
EM: Round [248] log likelihood: -7639.046868
EM: Round [249] log likelihood: -7639.043511
EM: Round [250] log likelihood: -7639.040167
EM: Round [251] log likelihood: -7639.036838
EM: Round [252] log likelihood: -7639.033523
EM: Round [253] log likelihood: -7639.030222
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EM: Round [716] log likelihood: -7638.290157
EM: Round [717] log likelihood: -7638.289458
EM: Round [718] log likelihood: -7638.288762
EM: Round [719] log likelihood: -7638.288068
EM: Round [720] log likelihood: -7638.287375
EM: Round [721] log likelihood: -7638.286685
EM: Round [722] log likelihood: -7638.285996
EM: Round [723] log likelihood: -7638.285310
EM: Round [724] log likelihood: -7638.284625
EM: Round [725] log likelihood: -7638.283943
EM: Round [726] log likelihood: -7638.283262
EM: Round [727] log likelihood: -7638.282584
EM: Round [728] log likelihood: -7638.281907
EM: Round [729] log likelihood: -7638.281233
EM: Round [730] log likelihood: -7638.280560
EM: Round [731] log likelihood: -7638.279889
EM: Round [732] log likelihood: -7638.279220
EM: Round [733] log likelihood: -7638.278554
EM: Round [734] log likelihood: -7638.277889
EM: Round [735] log likelihood: -7638.277225
EM: Round [736] log likelihood: -7638.276564
EM: Round [737] log likelihood: -7638.275905
EM: Round [738] log likelihood: -7638.275248
EM: Round [739] log likelihood: -7638.274592
EM: Round [740] log likelihood: -7638.273939
EM: Round [741] log likelihood: -7638.273287
EM: Round [742] log likelihood: -7638.272637
EM: Round [743] log likelihood: -7638.271989
EM: Round [744] log likelihood: -7638.271343
EM: Round [745] log likelihood: -7638.270699
EM: Round [746] log likelihood: -7638.270056
EM: Round [747] log likelihood: -7638.269416
EM: Round [748] log likelihood: -7638.268777
EM: Round [749] log likelihood: -7638.268140
EM: Round [750] log likelihood: -7638.267505
EM: Round [751] log likelihood: -7638.266871
EM: Round [752] log likelihood: -7638.266240
EM: Round [753] log likelihood: -7638.265610
EM: Round [754] log likelihood: -7638.264982
EM: Round [755] log likelihood: -7638.264356
EM: Round [756] log likelihood: -7638.263732
EM: Round [757] log likelihood: -7638.263110
EM: Round [758] log likelihood: -7638.262489
EM: Round [759] log likelihood: -7638.261870
EM: Round [760] log likelihood: -7638.261253
EM: Round [761] log likelihood: -7638.260637
EM: Round [762] log likelihood: -7638.260023
EM: Round [763] log likelihood: -7638.259412
EM: Round [764] log likelihood: -7638.258801
EM: Round [765] log likelihood: -7638.258193
EM: Round [766] log likelihood: -7638.257586
EM: Round [767] log likelihood: -7638.256981
EM: Round [768] log likelihood: -7638.256378
EM: Round [769] log likelihood: -7638.255776
EM: Round [770] log likelihood: -7638.255177
EM: Round [771] log likelihood: -7638.254578
EM: Round [772] log likelihood: -7638.253982
EM: Round [773] log likelihood: -7638.253387
EM: Round [774] log likelihood: -7638.252794
EM: Round [775] log likelihood: -7638.252203
EM: Round [776] log likelihood: -7638.251613
EM: Round [777] log likelihood: -7638.251025
EM: Round [778] log likelihood: -7638.250439
EM: Round [779] log likelihood: -7638.249854
EM: Round [780] log likelihood: -7638.249271
EM: Round [781] log likelihood: -7638.248690
EM: Round [782] log likelihood: -7638.248110
EM: Round [783] log likelihood: -7638.247532
EM: Round [784] log likelihood: -7638.246955
EM: Round [785] log likelihood: -7638.246381
EM: Round [786] log likelihood: -7638.245807
EM: Round [787] log likelihood: -7638.245236
EM: Round [788] log likelihood: -7638.244666
EM: Round [789] log likelihood: -7638.244097
EM: Round [790] log likelihood: -7638.243531
EM: Round [791] log likelihood: -7638.242966
EM: Round [792] log likelihood: -7638.242402
EM: Round [793] log likelihood: -7638.241840
EM: Round [794] log likelihood: -7638.241280
EM: Round [795] log likelihood: -7638.240721
EM: Round [796] log likelihood: -7638.240164
EM: Round [797] log likelihood: -7638.239608
EM: Round [798] log likelihood: -7638.239054
EM: Round [799] log likelihood: -7638.238502
EM: Round [800] log likelihood: -7638.237951
EM: Round [801] log likelihood: -7638.237401
EM: Round [802] log likelihood: -7638.236854
EM: Round [803] log likelihood: -7638.236307
EM: Round [804] log likelihood: -7638.235762
EM: Round [805] log likelihood: -7638.235219
EM: Round [806] log likelihood: -7638.234678
EM: Round [807] log likelihood: -7638.234137
EM: Round [808] log likelihood: -7638.233599
EM: Round [809] log likelihood: -7638.233062
EM: Round [810] log likelihood: -7638.232526
EM: Round [811] log likelihood: -7638.231992
EM: Round [812] log likelihood: -7638.231459
EM: Round [813] log likelihood: -7638.230928
EM: Round [814] log likelihood: -7638.230399
EM: Round [815] log likelihood: -7638.229870
EM: Round [816] log likelihood: -7638.229344
EM: Round [817] log likelihood: -7638.228819
EM: Round [818] log likelihood: -7638.228295
EM: Round [819] log likelihood: -7638.227773
EM: Round [820] log likelihood: -7638.227252
EM: Round [821] log likelihood: -7638.226733
EM: Round [822] log likelihood: -7638.226215
EM: Round [823] log likelihood: -7638.225698
EM: Round [824] log likelihood: -7638.225183
EM: Round [825] log likelihood: -7638.224670
EM: Round [826] log likelihood: -7638.224158
EM: Round [827] log likelihood: -7638.223647
EM: Round [828] log likelihood: -7638.223138
EM: Round [829] log likelihood: -7638.222630
EM: Round [830] log likelihood: -7638.222124
EM: Round [831] log likelihood: -7638.221619
EM: Round [832] log likelihood: -7638.221115
EM: Round [833] log likelihood: -7638.220613
EM: Round [834] log likelihood: -7638.220112
EM: Round [835] log likelihood: -7638.219613
EM: Round [836] log likelihood: -7638.219115
EM: Round [837] log likelihood: -7638.218619
EM: Round [838] log likelihood: -7638.218124
EM: Round [839] log likelihood: -7638.217630
EM: Round [840] log likelihood: -7638.217137
EM: Round [841] log likelihood: -7638.216646
EM: Round [842] log likelihood: -7638.216157
EM: Round [843] log likelihood: -7638.215668
EM: Round [844] log likelihood: -7638.215181
EM: Round [845] log likelihood: -7638.214696
EM: Round [846] log likelihood: -7638.214212
EM: Round [847] log likelihood: -7638.213729
EM: Round [848] log likelihood: -7638.213247
EM: Round [849] log likelihood: -7638.212767
EM: Round [850] log likelihood: -7638.212288
EM: Round [851] log likelihood: -7638.211811
EM: Round [852] log likelihood: -7638.211335
EM: Round [853] log likelihood: -7638.210860
EM: Round [854] log likelihood: -7638.210386
EM: Round [855] log likelihood: -7638.209914
EM: Round [856] log likelihood: -7638.209443
EM: Round [857] log likelihood: -7638.208973
EM: Round [858] log likelihood: -7638.208505
EM: Round [859] log likelihood: -7638.208038
EM: Round [860] log likelihood: -7638.207572
EM: Round [861] log likelihood: -7638.207108
EM: Round [862] log likelihood: -7638.206645
EM: Round [863] log likelihood: -7638.206183
EM: Round [864] log likelihood: -7638.205723
EM: Round [865] log likelihood: -7638.205263
EM: Round [866] log likelihood: -7638.204805
EM: Round [867] log likelihood: -7638.204349
EM: Round [868] log likelihood: -7638.203893
EM: Round [869] log likelihood: -7638.203439
EM: Round [870] log likelihood: -7638.202986
EM: Round [871] log likelihood: -7638.202534
EM: Round [872] log likelihood: -7638.202084
EM: Round [873] log likelihood: -7638.201635
EM: Round [874] log likelihood: -7638.201187
EM: Round [875] log likelihood: -7638.200740
EM: Round [876] log likelihood: -7638.200295
EM: Round [877] log likelihood: -7638.199850
EM: Round [878] log likelihood: -7638.199407
EM: Round [879] log likelihood: -7638.198965
EM: Round [880] log likelihood: -7638.198525
EM: Round [881] log likelihood: -7638.198086
EM: Round [882] log likelihood: -7638.197647
EM: Round [883] log likelihood: -7638.197211
EM: Round [884] log likelihood: -7638.196775
EM: Round [885] log likelihood: -7638.196340
EM: Round [886] log likelihood: -7638.195907
EM: Round [887] log likelihood: -7638.195475
EM: Round [888] log likelihood: -7638.195044
EM: Round [889] log likelihood: -7638.194614
EM: Round [890] log likelihood: -7638.194186
EM: Round [891] log likelihood: -7638.193758
EM: Round [892] log likelihood: -7638.193332
EM: Round [893] log likelihood: -7638.192907
EM: Round [894] log likelihood: -7638.192483
EM: Round [895] log likelihood: -7638.192061
EM: Round [896] log likelihood: -7638.191639
EM: Round [897] log likelihood: -7638.191219
EM: Round [898] log likelihood: -7638.190800
EM: Round [899] log likelihood: -7638.190382
EM: Round [900] log likelihood: -7638.189965
EM: Round [901] log likelihood: -7638.189549
EM: Round [902] log likelihood: -7638.189134
EM: Round [903] log likelihood: -7638.188721
EM: Round [904] log likelihood: -7638.188309
EM: Round [905] log likelihood: -7638.187897
EM: Round [906] log likelihood: -7638.187487
EM: Round [907] log likelihood: -7638.187078
EM: Round [908] log likelihood: -7638.186671
EM: Round [909] log likelihood: -7638.186264
EM: Round [910] log likelihood: -7638.185858
EM: Round [911] log likelihood: -7638.185454
EM: Round [912] log likelihood: -7638.185051
EM: Round [913] log likelihood: -7638.184648
EM: Round [914] log likelihood: -7638.184247
EM: Round [915] log likelihood: -7638.183847
EM: Round [916] log likelihood: -7638.183448
EM: Round [917] log likelihood: -7638.183050
EM: Round [918] log likelihood: -7638.182654
EM: Round [919] log likelihood: -7638.182258
EM: Round [920] log likelihood: -7638.181863
EM: Round [921] log likelihood: -7638.181470
EM: Round [922] log likelihood: -7638.181078
EM: Round [923] log likelihood: -7638.180686
EM: Round [924] log likelihood: -7638.180296
EM: Round [925] log likelihood: -7638.179907
EM: Round [926] log likelihood: -7638.179519
EM: Round [927] log likelihood: -7638.179132
EM: Round [928] log likelihood: -7638.178746
EM: Round [929] log likelihood: -7638.178361
EM: Round [930] log likelihood: -7638.177977
EM: Round [931] log likelihood: -7638.177594
EM: Round [932] log likelihood: -7638.177212
EM: Round [933] log likelihood: -7638.176831
EM: Round [934] log likelihood: -7638.176452
EM: Round [935] log likelihood: -7638.176073
EM: Round [936] log likelihood: -7638.175695
EM: Round [937] log likelihood: -7638.175319
EM: Round [938] log likelihood: -7638.174943
EM: Round [939] log likelihood: -7638.174569
EM: Round [940] log likelihood: -7638.174195
EM: Round [941] log likelihood: -7638.173822
EM: Round [942] log likelihood: -7638.173451
EM: Round [943] log likelihood: -7638.173080
EM: Round [944] log likelihood: -7638.172711
EM: Round [945] log likelihood: -7638.172343
EM: Round [946] log likelihood: -7638.171975
EM: Round [947] log likelihood: -7638.171609
EM: Round [948] log likelihood: -7638.171243
EM: Round [949] log likelihood: -7638.170879
EM: Round [950] log likelihood: -7638.170515
EM: Round [951] log likelihood: -7638.170153
EM: Round [952] log likelihood: -7638.169791
EM: Round [953] log likelihood: -7638.169431
EM: Round [954] log likelihood: -7638.169071
EM: Round [955] log likelihood: -7638.168713
EM: Round [956] log likelihood: -7638.168355
EM: Round [957] log likelihood: -7638.167999
EM: Round [958] log likelihood: -7638.167643
EM: Round [959] log likelihood: -7638.167288
EM: Round [960] log likelihood: -7638.166935
EM: Round [961] log likelihood: -7638.166582
EM: Round [962] log likelihood: -7638.166230
EM: Round [963] log likelihood: -7638.165879
EM: Round [964] log likelihood: -7638.165529
EM: Round [965] log likelihood: -7638.165181
EM: Round [966] log likelihood: -7638.164833
EM: Round [967] log likelihood: -7638.164486
EM: Round [968] log likelihood: -7638.164140
EM: Round [969] log likelihood: -7638.163794
EM: Round [970] log likelihood: -7638.163450
EM: Round [971] log likelihood: -7638.163107
EM: Round [972] log likelihood: -7638.162765
EM: Round [973] log likelihood: -7638.162423
EM: Round [974] log likelihood: -7638.162083
EM: Round [975] log likelihood: -7638.161743
EM: Round [976] log likelihood: -7638.161405
EM: Round [977] log likelihood: -7638.161067
EM: Round [978] log likelihood: -7638.160730
EM: Round [979] log likelihood: -7638.160394
EM: Round [980] log likelihood: -7638.160059
EM: Round [981] log likelihood: -7638.159725
EM: Round [982] log likelihood: -7638.159392
EM: Round [983] log likelihood: -7638.159060
EM: Round [984] log likelihood: -7638.158729
EM: Round [985] log likelihood: -7638.158398
EM: Round [986] log likelihood: -7638.158069
EM: Round [987] log likelihood: -7638.157740
EM: Round [988] log likelihood: -7638.157412
EM: Round [989] log likelihood: -7638.157085
EM: Round [990] log likelihood: -7638.156759
EM: Round [991] log likelihood: -7638.156434
EM: Round [992] log likelihood: -7638.156110
EM: Round [993] log likelihood: -7638.155787
EM: Round [994] log likelihood: -7638.155464
EM: Round [995] log likelihood: -7638.155142
EM: Round [996] log likelihood: -7638.154822
EM: Round [997] log likelihood: -7638.154502
EM: Round [998] log likelihood: -7638.154183
EM: Round [999] log likelihood: -7638.153865
EM: Round [1000] log likelihood: -7638.153547
EM: Round [1001] log likelihood: -7638.153231
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz: 229586432
Execution Time = 4.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa --gtf /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fa --gtf /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf > /tmp/nxf.vuGnvWu9DD/fi_workdir/microH.dat
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.vuGnvWu9DD/fi_workdir/microH.dat /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/fi_workdir/microH.dat /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.vuGnvWu9DD --json_outfile /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00658_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.vuGnvWu9DD --json_outfile /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00658_B23MVV7LT4_1
Running: touch /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00658_B23MVV7LT4_1 --html_output /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00658_B23MVV7LT4_1 --html_output /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000280639.1]
WARNING, no entry stored in dbm for [ENSG00000280639.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.vuGnvWu9DD/ctat_genome_lib_build_dir > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.vuGnvWu9DD/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory