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/59/eec142b236511253a05b82223a21f4/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/6375487ccdea12e4de2c836380f577/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/808bdad754efabbe9d85a0a9671b5b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/eec142b236511253a05b82223a21f4/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/808bdad754efabbe9d85a0a9671b5b/.command.run
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/cytoBand.txt
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.YrOfHpI81T/fi_workdir --reads "/tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:15:01 ..... started STAR run
Jun 08 10:15:01 ..... loading genome
Jun 08 10:16:44 ... generating Suffix Array index
Jun 08 10:20:27 ... completed Suffix Array index
Jun 08 10:20:28 ..... processing annotations GTF
Jun 08 10:20:28 ..... inserting junctions into the genome indices
Jun 08 10:21:29 ..... started mapping
Jun 08 10:43:12 ..... finished mapping
Jun 08 10:43:14 ..... started sorting BAM
Jun 08 10:43:15 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 28.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.YrOfHpI81T/fi_workdir --reads "/tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:43:29 : INFO : Done.
Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[2880000] -done parsing /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 9365,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'exons hit < 2' => 7,
'num genes matched < 2' => 14,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 23,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 394,
'small anchor length' => 78,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 18,
'low complexity anchor region' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 22,
'seq-similar region overlap' => 548,
'excessive soft clipping' => 9435,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
' ** passed ** ' => 11820
};
-writing fusion junction support info.
Execution Time = 1.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[57000] -fusion SPANNING read extraction for scaff: CELF4--TPGS2
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[21000] -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6
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[26000] -fusion SPANNING read extraction for scaff: GUSBP13--NAIP
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[50000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[57000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[59000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[68000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA13
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[66000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC1
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[60000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC2
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[94000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[53000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[46000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[61000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[50000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[23000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[23000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[94000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[46000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[61000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[53000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[50000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[94000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[53000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[46000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[47000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[33000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[61000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[50000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[293000] -fusion SPANNING read extraction for scaff: PRPH--TUBA1C
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[87000] -fusion SPANNING read extraction for scaff: PRPH--AC125611.4
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[30000] -fusion SPANNING read extraction for scaff: PSMD14--EXOC6B
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[50000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[42000] -fusion SPANNING read extraction for scaff: SYNM--AL691515.1
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[16000] -fusion SPANNING read extraction for scaff: TAB1--XPNPEP3
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[25000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[71000] -fusion SPANNING read extraction for scaff: TTC28--MN1
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[167000] -fusion SPANNING read extraction for scaff: ZNF638--TTC21B-AS1
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[206000] -fusion SPANNING read extraction for scaff: ZNF638--TTC21B
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 12694,
'seq similar region alignment' => 242443
};
Execution Time = 3.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4051.109390
EM: Round [1] log likelihood: -4050.658178
EM: Round [2] log likelihood: -4050.329496
EM: Round [3] log likelihood: -4050.032132
EM: Round [4] log likelihood: -4049.761974
EM: Round [5] log likelihood: -4049.515558
EM: Round [6] log likelihood: -4049.289916
EM: Round [7] log likelihood: -4049.082498
EM: Round [8] log likelihood: -4048.891104
EM: Round [9] log likelihood: -4048.713834
EM: Round [10] log likelihood: -4048.549036
EM: Round [11] log likelihood: -4048.395280
EM: Round [12] log likelihood: -4048.251317
EM: Round [13] log likelihood: -4048.116062
EM: Round [14] log likelihood: -4047.988562
EM: Round [15] log likelihood: -4047.867989
EM: Round [16] log likelihood: -4047.753614
EM: Round [17] log likelihood: -4047.644799
EM: Round [18] log likelihood: -4047.540986
EM: Round [19] log likelihood: -4047.441681
EM: Round [20] log likelihood: -4047.346454
EM: Round [21] log likelihood: -4047.254922
EM: Round [22] log likelihood: -4047.166751
EM: Round [23] log likelihood: -4047.081646
EM: Round [24] log likelihood: -4046.999345
EM: Round [25] log likelihood: -4046.919617
EM: Round [26] log likelihood: -4046.842260
EM: Round [27] log likelihood: -4046.767093
EM: Round [28] log likelihood: -4046.693957
EM: Round [29] log likelihood: -4046.622710
EM: Round [30] log likelihood: -4046.553226
EM: Round [31] log likelihood: -4046.485394
EM: Round [32] log likelihood: -4046.419115
EM: Round [33] log likelihood: -4046.354300
EM: Round [34] log likelihood: -4046.290870
EM: Round [35] log likelihood: -4046.228754
EM: Round [36] log likelihood: -4046.167890
EM: Round [37] log likelihood: -4046.108220
EM: Round [38] log likelihood: -4046.049694
EM: Round [39] log likelihood: -4045.992265
EM: Round [40] log likelihood: -4045.935892
EM: Round [41] log likelihood: -4045.880537
EM: Round [42] log likelihood: -4045.826165
EM: Round [43] log likelihood: -4045.772746
EM: Round [44] log likelihood: -4045.720251
EM: Round [45] log likelihood: -4045.668653
EM: Round [46] log likelihood: -4045.617928
EM: Round [47] log likelihood: -4045.568054
EM: Round [48] log likelihood: -4045.519010
EM: Round [49] log likelihood: -4045.470776
EM: Round [50] log likelihood: -4045.423335
EM: Round [51] log likelihood: -4045.376668
EM: Round [52] log likelihood: -4045.330761
EM: Round [53] log likelihood: -4045.285597
EM: Round [54] log likelihood: -4045.241163
EM: Round [55] log likelihood: -4045.197444
EM: Round [56] log likelihood: -4045.154427
EM: Round [57] log likelihood: -4045.112100
EM: Round [58] log likelihood: -4045.070450
EM: Round [59] log likelihood: -4045.029465
EM: Round [60] log likelihood: -4044.989135
EM: Round [61] log likelihood: -4044.949447
EM: Round [62] log likelihood: -4044.910391
EM: Round [63] log likelihood: -4044.871957
EM: Round [64] log likelihood: -4044.834135
EM: Round [65] log likelihood: -4044.796913
EM: Round [66] log likelihood: -4044.760283
EM: Round [67] log likelihood: -4044.724236
EM: Round [68] log likelihood: -4044.688760
EM: Round [69] log likelihood: -4044.653848
EM: Round [70] log likelihood: -4044.619490
EM: Round [71] log likelihood: -4044.585678
EM: Round [72] log likelihood: -4044.552401
EM: Round [73] log likelihood: -4044.519653
EM: Round [74] log likelihood: -4044.487424
EM: Round [75] log likelihood: -4044.455705
EM: Round [76] log likelihood: -4044.424489
EM: Round [77] log likelihood: -4044.393767
EM: Round [78] log likelihood: -4044.363531
EM: Round [79] log likelihood: -4044.333774
EM: Round [80] log likelihood: -4044.304487
EM: Round [81] log likelihood: -4044.275663
EM: Round [82] log likelihood: -4044.247294
EM: Round [83] log likelihood: -4044.219372
EM: Round [84] log likelihood: -4044.191891
EM: Round [85] log likelihood: -4044.164842
EM: Round [86] log likelihood: -4044.138219
EM: Round [87] log likelihood: -4044.112015
EM: Round [88] log likelihood: -4044.086222
EM: Round [89] log likelihood: -4044.060833
EM: Round [90] log likelihood: -4044.035843
EM: Round [91] log likelihood: -4044.011243
EM: Round [92] log likelihood: -4043.987028
EM: Round [93] log likelihood: -4043.963191
EM: Round [94] log likelihood: -4043.939725
EM: Round [95] log likelihood: -4043.916624
EM: Round [96] log likelihood: -4043.893883
EM: Round [97] log likelihood: -4043.871494
EM: Round [98] log likelihood: -4043.849452
EM: Round [99] log likelihood: -4043.827751
EM: Round [100] log likelihood: -4043.806385
EM: Round [101] log likelihood: -4043.785348
EM: Round [102] log likelihood: -4043.764634
EM: Round [103] log likelihood: -4043.744239
EM: Round [104] log likelihood: -4043.724156
EM: Round [105] log likelihood: -4043.704381
EM: Round [106] log likelihood: -4043.684907
EM: Round [107] log likelihood: -4043.665729
EM: Round [108] log likelihood: -4043.646844
EM: Round [109] log likelihood: -4043.628244
EM: Round [110] log likelihood: -4043.609926
EM: Round [111] log likelihood: -4043.591885
EM: Round [112] log likelihood: -4043.574115
EM: Round [113] log likelihood: -4043.556613
EM: Round [114] log likelihood: -4043.539373
EM: Round [115] log likelihood: -4043.522391
EM: Round [116] log likelihood: -4043.505662
EM: Round [117] log likelihood: -4043.489183
EM: Round [118] log likelihood: -4043.472948
EM: Round [119] log likelihood: -4043.456954
EM: Round [120] log likelihood: -4043.441196
EM: Round [121] log likelihood: -4043.425670
EM: Round [122] log likelihood: -4043.410373
EM: Round [123] log likelihood: -4043.395300
EM: Round [124] log likelihood: -4043.380447
EM: Round [125] log likelihood: -4043.365811
EM: Round [126] log likelihood: -4043.351388
EM: Round [127] log likelihood: -4043.337174
EM: Round [128] log likelihood: -4043.323166
EM: Round [129] log likelihood: -4043.309360
EM: Round [130] log likelihood: -4043.295753
EM: Round [131] log likelihood: -4043.282341
EM: Round [132] log likelihood: -4043.269121
EM: Round [133] log likelihood: -4043.256090
EM: Round [134] log likelihood: -4043.243244
EM: Round [135] log likelihood: -4043.230580
EM: Round [136] log likelihood: -4043.218095
EM: Round [137] log likelihood: -4043.205787
EM: Round [138] log likelihood: -4043.193652
EM: Round [139] log likelihood: -4043.181687
EM: Round [140] log likelihood: -4043.169889
EM: Round [141] log likelihood: -4043.158256
EM: Round [142] log likelihood: -4043.146785
EM: Round [143] log likelihood: -4043.135472
EM: Round [144] log likelihood: -4043.124316
EM: Round [145] log likelihood: -4043.113314
EM: Round [146] log likelihood: -4043.102463
EM: Round [147] log likelihood: -4043.091761
EM: Round [148] log likelihood: -4043.081205
EM: Round [149] log likelihood: -4043.070792
EM: Round [150] log likelihood: -4043.060521
EM: Round [151] log likelihood: -4043.050390
EM: Round [152] log likelihood: -4043.040394
EM: Round [153] log likelihood: -4043.030534
EM: Round [154] log likelihood: -4043.020806
EM: Round [155] log likelihood: -4043.011207
EM: Round [156] log likelihood: -4043.001737
EM: Round [157] log likelihood: -4042.992393
EM: Round [158] log likelihood: -4042.983173
EM: Round [159] log likelihood: -4042.974074
EM: Round [160] log likelihood: -4042.965096
EM: Round [161] log likelihood: -4042.956235
EM: Round [162] log likelihood: -4042.947491
EM: Round [163] log likelihood: -4042.938861
EM: Round [164] log likelihood: -4042.930343
EM: Round [165] log likelihood: -4042.921935
EM: Round [166] log likelihood: -4042.913637
EM: Round [167] log likelihood: -4042.905446
EM: Round [168] log likelihood: -4042.897360
EM: Round [169] log likelihood: -4042.889377
EM: Round [170] log likelihood: -4042.881497
EM: Round [171] log likelihood: -4042.873717
EM: Round [172] log likelihood: -4042.866037
EM: Round [173] log likelihood: -4042.858453
EM: Round [174] log likelihood: -4042.850966
EM: Round [175] log likelihood: -4042.843573
EM: Round [176] log likelihood: -4042.836272
EM: Round [177] log likelihood: -4042.829063
EM: Round [178] log likelihood: -4042.821945
EM: Round [179] log likelihood: -4042.814914
EM: Round [180] log likelihood: -4042.807972
EM: Round [181] log likelihood: -4042.801115
EM: Round [182] log likelihood: -4042.794343
EM: Round [183] log likelihood: -4042.787654
EM: Round [184] log likelihood: -4042.781047
EM: Round [185] log likelihood: -4042.774521
EM: Round [186] log likelihood: -4042.768075
EM: Round [187] log likelihood: -4042.761707
EM: Round [188] log likelihood: -4042.755417
EM: Round [189] log likelihood: -4042.749203
EM: Round [190] log likelihood: -4042.743063
EM: Round [191] log likelihood: -4042.736998
EM: Round [192] log likelihood: -4042.731005
EM: Round [193] log likelihood: -4042.725084
EM: Round [194] log likelihood: -4042.719234
EM: Round [195] log likelihood: -4042.713454
EM: Round [196] log likelihood: -4042.707742
EM: Round [197] log likelihood: -4042.702097
EM: Round [198] log likelihood: -4042.696519
EM: Round [199] log likelihood: -4042.691007
EM: Round [200] log likelihood: -4042.685560
EM: Round [201] log likelihood: -4042.680176
EM: Round [202] log likelihood: -4042.674855
EM: Round [203] log likelihood: -4042.669597
EM: Round [204] log likelihood: -4042.664399
EM: Round [205] log likelihood: -4042.659261
EM: Round [206] log likelihood: -4042.654183
EM: Round [207] log likelihood: -4042.649163
EM: Round [208] log likelihood: -4042.644201
EM: Round [209] log likelihood: -4042.639296
EM: Round [210] log likelihood: -4042.634447
EM: Round [211] log likelihood: -4042.629653
EM: Round [212] log likelihood: -4042.624914
EM: Round [213] log likelihood: -4042.620229
EM: Round [214] log likelihood: -4042.615596
EM: Round [215] log likelihood: -4042.611016
EM: Round [216] log likelihood: -4042.606488
EM: Round [217] log likelihood: -4042.602010
EM: Round [218] log likelihood: -4042.597583
EM: Round [219] log likelihood: -4042.593205
EM: Round [220] log likelihood: -4042.588875
EM: Round [221] log likelihood: -4042.584594
EM: Round [222] log likelihood: -4042.580361
EM: Round [223] log likelihood: -4042.576174
EM: Round [224] log likelihood: -4042.572034
EM: Round [225] log likelihood: -4042.567939
EM: Round [226] log likelihood: -4042.563889
EM: Round [227] log likelihood: -4042.559883
EM: Round [228] log likelihood: -4042.555922
EM: Round [229] log likelihood: -4042.552003
EM: Round [230] log likelihood: -4042.548128
EM: Round [231] log likelihood: -4042.544294
EM: Round [232] log likelihood: -4042.540502
EM: Round [233] log likelihood: -4042.536751
EM: Round [234] log likelihood: -4042.533040
EM: Round [235] log likelihood: -4042.529370
EM: Round [236] log likelihood: -4042.525738
EM: Round [237] log likelihood: -4042.522146
EM: Round [238] log likelihood: -4042.518592
EM: Round [239] log likelihood: -4042.515076
EM: Round [240] log likelihood: -4042.511598
EM: Round [241] log likelihood: -4042.508156
EM: Round [242] log likelihood: -4042.504751
EM: Round [243] log likelihood: -4042.501382
EM: Round [244] log likelihood: -4042.498049
EM: Round [245] log likelihood: -4042.494750
EM: Round [246] log likelihood: -4042.491486
EM: Round [247] log likelihood: -4042.488257
EM: Round [248] log likelihood: -4042.485061
EM: Round [249] log likelihood: -4042.481899
EM: Round [250] log likelihood: -4042.478770
EM: Round [251] log likelihood: -4042.475673
EM: Round [252] log likelihood: -4042.472608
EM: Round [253] log likelihood: -4042.469576
EM: Round [254] log likelihood: -4042.466574
EM: Round [255] log likelihood: -4042.463604
EM: Round [256] log likelihood: -4042.460664
EM: Round [257] log likelihood: -4042.457754
EM: Round [258] log likelihood: -4042.454874
EM: Round [259] log likelihood: -4042.452024
EM: Round [260] log likelihood: -4042.449203
EM: Round [261] log likelihood: -4042.446411
EM: Round [262] log likelihood: -4042.443647
EM: Round [263] log likelihood: -4042.440911
EM: Round [264] log likelihood: -4042.438203
EM: Round [265] log likelihood: -4042.435522
EM: Round [266] log likelihood: -4042.432869
EM: Round [267] log likelihood: -4042.430242
EM: Round [268] log likelihood: -4042.427642
EM: Round [269] log likelihood: -4042.425067
EM: Round [270] log likelihood: -4042.422519
EM: Round [271] log likelihood: -4042.419996
EM: Round [272] log likelihood: -4042.417499
EM: Round [273] log likelihood: -4042.415026
EM: Round [274] log likelihood: -4042.412578
EM: Round [275] log likelihood: -4042.410155
EM: Round [276] log likelihood: -4042.407755
EM: Round [277] log likelihood: -4042.405379
EM: Round [278] log likelihood: -4042.403027
EM: Round [279] log likelihood: -4042.400698
EM: Round [280] log likelihood: -4042.398392
EM: Round [281] log likelihood: -4042.396109
EM: Round [282] log likelihood: -4042.393848
EM: Round [283] log likelihood: -4042.391609
EM: Round [284] log likelihood: -4042.389393
EM: Round [285] log likelihood: -4042.387198
EM: Round [286] log likelihood: -4042.385024
EM: Round [287] log likelihood: -4042.382872
EM: Round [288] log likelihood: -4042.380741
EM: Round [289] log likelihood: -4042.378630
EM: Round [290] log likelihood: -4042.376540
EM: Round [291] log likelihood: -4042.374470
EM: Round [292] log likelihood: -4042.372420
EM: Round [293] log likelihood: -4042.370390
EM: Round [294] log likelihood: -4042.368379
EM: Round [295] log likelihood: -4042.366388
EM: Round [296] log likelihood: -4042.364416
EM: Round [297] log likelihood: -4042.362463
EM: Round [298] log likelihood: -4042.360529
EM: Round [299] log likelihood: -4042.358613
EM: Round [300] log likelihood: -4042.356716
EM: Round [301] log likelihood: -4042.354837
EM: Round [302] log likelihood: -4042.352975
EM: Round [303] log likelihood: -4042.351132
EM: Round [304] log likelihood: -4042.349306
EM: Round [305] log likelihood: -4042.347497
EM: Round [306] log likelihood: -4042.345705
EM: Round [307] log likelihood: -4042.343930
EM: Round [308] log likelihood: -4042.342173
EM: Round [309] log likelihood: -4042.340431
EM: Round [310] log likelihood: -4042.338706
EM: Round [311] log likelihood: -4042.336998
EM: Round [312] log likelihood: -4042.335305
EM: Round [313] log likelihood: -4042.333629
EM: Round [314] log likelihood: -4042.331968
EM: Round [315] log likelihood: -4042.330322
EM: Round [316] log likelihood: -4042.328692
EM: Round [317] log likelihood: -4042.327078
EM: Round [318] log likelihood: -4042.325478
EM: Round [319] log likelihood: -4042.323893
EM: Round [320] log likelihood: -4042.322323
EM: Round [321] log likelihood: -4042.320768
EM: Round [322] log likelihood: -4042.319227
EM: Round [323] log likelihood: -4042.317700
EM: Round [324] log likelihood: -4042.316187
EM: Round [325] log likelihood: -4042.314689
EM: Round [326] log likelihood: -4042.313204
EM: Round [327] log likelihood: -4042.311733
EM: Round [328] log likelihood: -4042.310275
EM: Round [329] log likelihood: -4042.308831
EM: Round [330] log likelihood: -4042.307400
EM: Round [331] log likelihood: -4042.305983
EM: Round [332] log likelihood: -4042.304578
EM: Round [333] log likelihood: -4042.303186
EM: Round [334] log likelihood: -4042.301807
EM: Round [335] log likelihood: -4042.300441
EM: Round [336] log likelihood: -4042.299087
EM: Round [337] log likelihood: -4042.297745
EM: Round [338] log likelihood: -4042.296415
EM: Round [339] log likelihood: -4042.295098
EM: Round [340] log likelihood: -4042.293793
EM: Round [341] log likelihood: -4042.292499
EM: Round [342] log likelihood: -4042.291217
EM: Round [343] log likelihood: -4042.289947
EM: Round [344] log likelihood: -4042.288688
EM: Round [345] log likelihood: -4042.287441
EM: Round [346] log likelihood: -4042.286204
EM: Round [347] log likelihood: -4042.284979
EM: Round [348] log likelihood: -4042.283765
EM: Round [349] log likelihood: -4042.282562
EM: Round [350] log likelihood: -4042.281370
EM: Round [351] log likelihood: -4042.280189
EM: Round [352] log likelihood: -4042.279018
EM: Round [353] log likelihood: -4042.277857
EM: Round [354] log likelihood: -4042.276707
EM: Round [355] log likelihood: -4042.275567
EM: Round [356] log likelihood: -4042.274437
EM: Round [357] log likelihood: -4042.273318
EM: Round [358] log likelihood: -4042.272208
EM: Round [359] log likelihood: -4042.271108
EM: Round [360] log likelihood: -4042.270018
EM: Round [361] log likelihood: -4042.268938
EM: Round [362] log likelihood: -4042.267867
EM: Round [363] log likelihood: -4042.266806
EM: Round [364] log likelihood: -4042.265754
EM: Round [365] log likelihood: -4042.264712
EM: Round [366] log likelihood: -4042.263678
EM: Round [367] log likelihood: -4042.262654
EM: Round [368] log likelihood: -4042.261639
EM: Round [369] log likelihood: -4042.260632
EM: Round [370] log likelihood: -4042.259635
EM: Round [371] log likelihood: -4042.258646
EM: Round [372] log likelihood: -4042.257666
EM: Round [373] log likelihood: -4042.256695
EM: Round [374] log likelihood: -4042.255732
EM: Round [375] log likelihood: -4042.254778
EM: Round [376] log likelihood: -4042.253832
EM: Round [377] log likelihood: -4042.252894
EM: Round [378] log likelihood: -4042.251964
EM: Round [379] log likelihood: -4042.251043
EM: Round [380] log likelihood: -4042.250129
EM: Round [381] log likelihood: -4042.249224
EM: Round [382] log likelihood: -4042.248326
EM: Round [383] log likelihood: -4042.247436
EM: Round [384] log likelihood: -4042.246554
EM: Round [385] log likelihood: -4042.245679
EM: Round [386] log likelihood: -4042.244812
EM: Round [387] log likelihood: -4042.243953
EM: Round [388] log likelihood: -4042.243101
EM: Round [389] log likelihood: -4042.242256
EM: Round [390] log likelihood: -4042.241419
EM: Round [391] log likelihood: -4042.240589
EM: Round [392] log likelihood: -4042.239766
EM: Round [393] log likelihood: -4042.238950
EM: Round [394] log likelihood: -4042.238141
EM: Round [395] log likelihood: -4042.237339
EM: Round [396] log likelihood: -4042.236544
EM: Round [397] log likelihood: -4042.235756
EM: Round [398] log likelihood: -4042.234974
EM: Round [399] log likelihood: -4042.234200
EM: Round [400] log likelihood: -4042.233432
EM: Round [401] log likelihood: -4042.232670
EM: Round [402] log likelihood: -4042.231915
EM: Round [403] log likelihood: -4042.231166
EM: Round [404] log likelihood: -4042.230424
EM: Round [405] log likelihood: -4042.229688
EM: Round [406] log likelihood: -4042.228958
EM: Round [407] log likelihood: -4042.228235
EM: Round [408] log likelihood: -4042.227518
EM: Round [409] log likelihood: -4042.226806
EM: Round [410] log likelihood: -4042.226101
EM: Round [411] log likelihood: -4042.225402
EM: Round [412] log likelihood: -4042.224709
EM: Round [413] log likelihood: -4042.224021
EM: Round [414] log likelihood: -4042.223340
EM: Round [415] log likelihood: -4042.222664
EM: Round [416] log likelihood: -4042.221994
EM: Round [417] log likelihood: -4042.221329
EM: Round [418] log likelihood: -4042.220670
EM: Round [419] log likelihood: -4042.220017
EM: Round [420] log likelihood: -4042.219369
EM: Round [421] log likelihood: -4042.218727
EM: Round [422] log likelihood: -4042.218089
EM: Round [423] log likelihood: -4042.217458
EM: Round [424] log likelihood: -4042.216831
EM: Round [425] log likelihood: -4042.216210
EM: Round [426] log likelihood: -4042.215594
EM: Round [427] log likelihood: -4042.214984
EM: Round [428] log likelihood: -4042.214378
EM: Round [429] log likelihood: -4042.213777
EM: Round [430] log likelihood: -4042.213182
EM: Round [431] log likelihood: -4042.212591
EM: Round [432] log likelihood: -4042.212005
EM: Round [433] log likelihood: -4042.211424
EM: Round [434] log likelihood: -4042.210848
EM: Round [435] log likelihood: -4042.210277
EM: Round [436] log likelihood: -4042.209711
EM: Round [437] log likelihood: -4042.209149
EM: Round [438] log likelihood: -4042.208592
EM: Round [439] log likelihood: -4042.208039
EM: Round [440] log likelihood: -4042.207491
EM: Round [441] log likelihood: -4042.206948
EM: Round [442] log likelihood: -4042.206409
EM: Round [443] log likelihood: -4042.205874
EM: Round [444] log likelihood: -4042.205344
EM: Round [445] log likelihood: -4042.204819
EM: Round [446] log likelihood: -4042.204297
EM: Round [447] log likelihood: -4042.203780
EM: Round [448] log likelihood: -4042.203268
EM: Round [449] log likelihood: -4042.202759
EM: Round [450] log likelihood: -4042.202255
EM: Round [451] log likelihood: -4042.201754
EM: Round [452] log likelihood: -4042.201258
EM: Round [453] log likelihood: -4042.200766
EM: Round [454] log likelihood: -4042.200278
EM: Round [455] log likelihood: -4042.199794
EM: Round [456] log likelihood: -4042.199314
EM: Round [457] log likelihood: -4042.198838
EM: Round [458] log likelihood: -4042.198365
EM: Round [459] log likelihood: -4042.197897
EM: Round [460] log likelihood: -4042.197432
EM: Round [461] log likelihood: -4042.196972
EM: Round [462] log likelihood: -4042.196515
EM: Round [463] log likelihood: -4042.196061
EM: Round [464] log likelihood: -4042.195612
EM: Round [465] log likelihood: -4042.195165
EM: Round [466] log likelihood: -4042.194723
EM: Round [467] log likelihood: -4042.194284
EM: Round [468] log likelihood: -4042.193849
EM: Round [469] log likelihood: -4042.193417
EM: Round [470] log likelihood: -4042.192989
EM: Round [471] log likelihood: -4042.192564
EM: Round [472] log likelihood: -4042.192143
EM: Round [473] log likelihood: -4042.191725
EM: Round [474] log likelihood: -4042.191311
EM: Round [475] log likelihood: -4042.190900
EM: Round [476] log likelihood: -4042.190492
EM: Round [477] log likelihood: -4042.190087
EM: Round [478] log likelihood: -4042.189686
EM: Round [479] log likelihood: -4042.189288
EM: Round [480] log likelihood: -4042.188893
EM: Round [481] log likelihood: -4042.188501
EM: Round [482] log likelihood: -4042.188112
EM: Round [483] log likelihood: -4042.187727
EM: Round [484] log likelihood: -4042.187345
EM: Round [485] log likelihood: -4042.186965
EM: Round [486] log likelihood: -4042.186589
EM: Round [487] log likelihood: -4042.186216
EM: Round [488] log likelihood: -4042.185846
EM: Round [489] log likelihood: -4042.185478
EM: Round [490] log likelihood: -4042.185114
EM: Round [491] log likelihood: -4042.184753
EM: Round [492] log likelihood: -4042.184394
EM: Round [493] log likelihood: -4042.184038
EM: Round [494] log likelihood: -4042.183685
EM: Round [495] log likelihood: -4042.183335
EM: Round [496] log likelihood: -4042.182988
EM: Round [497] log likelihood: -4042.182643
EM: Round [498] log likelihood: -4042.182302
EM: Round [499] log likelihood: -4042.181963
EM: Round [500] log likelihood: -4042.181626
EM: Round [501] log likelihood: -4042.181293
EM: Round [502] log likelihood: -4042.180961
EM: Round [503] log likelihood: -4042.180633
EM: Round [504] log likelihood: -4042.180307
EM: Round [505] log likelihood: -4042.179984
EM: Round [506] log likelihood: -4042.179663
EM: Round [507] log likelihood: -4042.179345
EM: Round [508] log likelihood: -4042.179029
EM: Round [509] log likelihood: -4042.178716
EM: Round [510] log likelihood: -4042.178405
EM: Round [511] log likelihood: -4042.178097
EM: Round [512] log likelihood: -4042.177791
EM: Round [513] log likelihood: -4042.177488
EM: Round [514] log likelihood: -4042.177187
EM: Round [515] log likelihood: -4042.176888
EM: Round [516] log likelihood: -4042.176592
EM: Round [517] log likelihood: -4042.176298
EM: Round [518] log likelihood: -4042.176006
EM: Round [519] log likelihood: -4042.175717
EM: Round [520] log likelihood: -4042.175430
EM: Round [521] log likelihood: -4042.175145
EM: Round [522] log likelihood: -4042.174862
EM: Round [523] log likelihood: -4042.174582
EM: Round [524] log likelihood: -4042.174303
EM: Round [525] log likelihood: -4042.174027
EM: Round [526] log likelihood: -4042.173753
EM: Round [527] log likelihood: -4042.173482
EM: Round [528] log likelihood: -4042.173212
EM: Round [529] log likelihood: -4042.172944
EM: Round [530] log likelihood: -4042.172679
EM: Round [531] log likelihood: -4042.172415
EM: Round [532] log likelihood: -4042.172154
EM: Round [533] log likelihood: -4042.171895
EM: Round [534] log likelihood: -4042.171637
EM: Round [535] log likelihood: -4042.171382
EM: Round [536] log likelihood: -4042.171129
EM: Round [537] log likelihood: -4042.170877
EM: Round [538] log likelihood: -4042.170628
EM: Round [539] log likelihood: -4042.170380
EM: Round [540] log likelihood: -4042.170135
EM: Round [541] log likelihood: -4042.169891
EM: Round [542] log likelihood: -4042.169649
EM: Round [543] log likelihood: -4042.169409
EM: Round [544] log likelihood: -4042.169171
EM: Round [545] log likelihood: -4042.168935
EM: Round [546] log likelihood: -4042.168701
EM: Round [547] log likelihood: -4042.168468
EM: Round [548] log likelihood: -4042.168237
EM: Round [549] log likelihood: -4042.168008
EM: Round [550] log likelihood: -4042.167781
EM: Round [551] log likelihood: -4042.167555
EM: Round [552] log likelihood: -4042.167332
EM: Round [553] log likelihood: -4042.167110
EM: Round [554] log likelihood: -4042.166889
EM: Round [555] log likelihood: -4042.166671
EM: Round [556] log likelihood: -4042.166453
EM: Round [557] log likelihood: -4042.166238
EM: Round [558] log likelihood: -4042.166024
EM: Round [559] log likelihood: -4042.165812
EM: Round [560] log likelihood: -4042.165602
EM: Round [561] log likelihood: -4042.165393
EM: Round [562] log likelihood: -4042.165186
EM: Round [563] log likelihood: -4042.164980
EM: Round [564] log likelihood: -4042.164776
EM: Round [565] log likelihood: -4042.164574
EM: Round [566] log likelihood: -4042.164373
EM: Round [567] log likelihood: -4042.164173
EM: Round [568] log likelihood: -4042.163975
EM: Round [569] log likelihood: -4042.163779
EM: Round [570] log likelihood: -4042.163584
EM: Round [571] log likelihood: -4042.163391
EM: Round [572] log likelihood: -4042.163199
EM: Round [573] log likelihood: -4042.163008
EM: Round [574] log likelihood: -4042.162819
EM: Round [575] log likelihood: -4042.162631
EM: Round [576] log likelihood: -4042.162445
EM: Round [577] log likelihood: -4042.162260
EM: Round [578] log likelihood: -4042.162077
EM: Round [579] log likelihood: -4042.161895
EM: Round [580] log likelihood: -4042.161714
EM: Round [581] log likelihood: -4042.161535
EM: Round [582] log likelihood: -4042.161357
EM: Round [583] log likelihood: -4042.161181
EM: Round [584] log likelihood: -4042.161005
EM: Round [585] log likelihood: -4042.160832
EM: Round [586] log likelihood: -4042.160659
EM: Round [587] log likelihood: -4042.160488
EM: Round [588] log likelihood: -4042.160318
EM: Round [589] log likelihood: -4042.160149
EM: Round [590] log likelihood: -4042.159982
EM: Round [591] log likelihood: -4042.159815
EM: Round [592] log likelihood: -4042.159650
EM: Round [593] log likelihood: -4042.159487
EM: Round [594] log likelihood: -4042.159324
EM: Round [595] log likelihood: -4042.159163
EM: Round [596] log likelihood: -4042.159003
EM: Round [597] log likelihood: -4042.158844
EM: Round [598] log likelihood: -4042.158686
EM: Round [599] log likelihood: -4042.158530
EM: Round [600] log likelihood: -4042.158375
EM: Round [601] log likelihood: -4042.158221
EM: Round [602] log likelihood: -4042.158068
EM: Round [603] log likelihood: -4042.157916
EM: Round [604] log likelihood: -4042.157765
EM: Round [605] log likelihood: -4042.157615
EM: Round [606] log likelihood: -4042.157467
EM: Round [607] log likelihood: -4042.157320
EM: Round [608] log likelihood: -4042.157173
EM: Round [609] log likelihood: -4042.157028
EM: Round [610] log likelihood: -4042.156884
EM: Round [611] log likelihood: -4042.156741
EM: Round [612] log likelihood: -4042.156599
EM: Round [613] log likelihood: -4042.156458
EM: Round [614] log likelihood: -4042.156319
EM: Round [615] log likelihood: -4042.156180
EM: Round [616] log likelihood: -4042.156042
EM: Round [617] log likelihood: -4042.155905
EM: Round [618] log likelihood: -4042.155770
EM: Round [619] log likelihood: -4042.155635
EM: Round [620] log likelihood: -4042.155501
EM: Round [621] log likelihood: -4042.155368
EM: Round [622] log likelihood: -4042.155237
EM: Round [623] log likelihood: -4042.155106
EM: Round [624] log likelihood: -4042.154976
EM: Round [625] log likelihood: -4042.154847
EM: Round [626] log likelihood: -4042.154719
EM: Round [627] log likelihood: -4042.154592
EM: Round [628] log likelihood: -4042.154466
EM: Round [629] log likelihood: -4042.154341
EM: Round [630] log likelihood: -4042.154217
EM: Round [631] log likelihood: -4042.154094
EM: Round [632] log likelihood: -4042.153972
EM: Round [633] log likelihood: -4042.153850
EM: Round [634] log likelihood: -4042.153730
EM: Round [635] log likelihood: -4042.153610
EM: Round [636] log likelihood: -4042.153491
EM: Round [637] log likelihood: -4042.153373
EM: Round [638] log likelihood: -4042.153256
EM: Round [639] log likelihood: -4042.153140
EM: Round [640] log likelihood: -4042.153025
EM: Round [641] log likelihood: -4042.152910
EM: Round [642] log likelihood: -4042.152797
EM: Round [643] log likelihood: -4042.152684
EM: Round [644] log likelihood: -4042.152572
EM: Round [645] log likelihood: -4042.152461
EM: Round [646] log likelihood: -4042.152351
EM: Round [647] log likelihood: -4042.152241
EM: Round [648] log likelihood: -4042.152132
EM: Round [649] log likelihood: -4042.152024
EM: Round [650] log likelihood: -4042.151917
EM: Round [651] log likelihood: -4042.151811
EM: Round [652] log likelihood: -4042.151705
EM: Round [653] log likelihood: -4042.151601
EM: Round [654] log likelihood: -4042.151497
EM: Round [655] log likelihood: -4042.151393
EM: Round [656] log likelihood: -4042.151291
EM: Round [657] log likelihood: -4042.151189
EM: Round [658] log likelihood: -4042.151088
EM: Round [659] log likelihood: -4042.150988
EM: Round [660] log likelihood: -4042.150888
EM: Stopping iterations at round 660 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir
-done, see /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2205.682388
EM: Round [1] log likelihood: -2205.682388
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 201017995
Execution Time = 3.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.YrOfHpI81T/fi_workdir/microH.dat
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.YrOfHpI81T/fi_workdir/microH.dat /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/fi_workdir/microH.dat /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.YrOfHpI81T --json_outfile /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.YrOfHpI81T --json_outfile /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.YrOfHpI81T/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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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 [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000237283.2]
WARNING, no entry stored in dbm for [ENSG00000237283.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000224490.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.YrOfHpI81T/ctat_genome_lib_build_dir > /tmp/nxf.YrOfHpI81T/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.YrOfHpI81T/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory