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/12/4355c33b7683209806e20cf4b8e5a7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/4355c33b7683209806e20cf4b8e5a7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/e6c9734b98fe81ad02554a1675aa28/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/ff28516c049681dbc11ee2908b5be8/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/ff28516c049681dbc11ee2908b5be8/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --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 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/cytoBand.txt
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.LWz6SM2kxe/fi_workdir --reads "/tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:39:37 ..... started STAR run
Jun 08 10:39:37 ..... loading genome
Jun 08 10:41:16 ... generating Suffix Array index
Jun 08 10:45:21 ... completed Suffix Array index
Jun 08 10:45:21 ..... processing annotations GTF
Jun 08 10:45:22 ..... inserting junctions into the genome indices
Jun 08 10:46:22 ..... started mapping
Jun 08 11:27:43 ..... finished mapping
Jun 08 11:27:44 ..... started sorting BAM
Jun 08 11:27:45 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 48.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.LWz6SM2kxe/fi_workdir --reads "/tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
11:27:59 : INFO : Done.
Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[2710000] -done parsing /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'small anchor length' => 33,
'num genes matched < 2' => 30,
'low complexity anchor region' => 10,
'seq-similar region overlap' => 884,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 180,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 41,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2252,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'per_id < 96' => 32732,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'exons hit < 2' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
' ** passed ** ' => 18180,
'excessive soft clipping' => 16568,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 1286
};
-writing fusion junction support info.
Execution Time = 1.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[471000] -fusion SPANNING read extraction for scaff: MEOX2--CRPPA
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[465000] -fusion SPANNING read extraction for scaff: MEOX2--AC006041.1
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[61000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[10000] -fusion SPANNING read extraction for scaff: OR8D1--OR8A1
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[116000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[133000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[116000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[81000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[98000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[82000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[38000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[26000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[26000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[32000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[139000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[37000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[138000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
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[6000] -fusion SPANNING read extraction for scaff: SLC5A4P1--OR8A1
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[108000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[49000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[14000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[15000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[65000] -fusion SPANNING read extraction for scaff: WASH3P--LINC01237
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[65000] -fusion SPANNING read extraction for scaff: WASH3P--LINC01880
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 5464,
'seq similar region alignment' => 107850
};
Execution Time = 2.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6034.275448
EM: Round [1] log likelihood: -6033.845861
EM: Round [2] log likelihood: -6033.515176
EM: Round [3] log likelihood: -6033.198294
EM: Round [4] log likelihood: -6032.891806
EM: Round [5] log likelihood: -6032.594629
EM: Round [6] log likelihood: -6032.305925
EM: Round [7] log likelihood: -6032.025018
EM: Round [8] log likelihood: -6031.751366
EM: Round [9] log likelihood: -6031.484539
EM: Round [10] log likelihood: -6031.224197
EM: Round [11] log likelihood: -6030.970074
EM: Round [12] log likelihood: -6030.721961
EM: Round [13] log likelihood: -6030.479696
EM: Round [14] log likelihood: -6030.243149
EM: Round [15] log likelihood: -6030.012218
EM: Round [16] log likelihood: -6029.786818
EM: Round [17] log likelihood: -6029.566875
EM: Round [18] log likelihood: -6029.352322
EM: Round [19] log likelihood: -6029.143097
EM: Round [20] log likelihood: -6028.939134
EM: Round [21] log likelihood: -6028.740370
EM: Round [22] log likelihood: -6028.546734
EM: Round [23] log likelihood: -6028.358152
EM: Round [24] log likelihood: -6028.174545
EM: Round [25] log likelihood: -6027.995828
EM: Round [26] log likelihood: -6027.821911
EM: Round [27] log likelihood: -6027.652699
EM: Round [28] log likelihood: -6027.488090
EM: Round [29] log likelihood: -6027.327982
EM: Round [30] log likelihood: -6027.172265
EM: Round [31] log likelihood: -6027.020828
EM: Round [32] log likelihood: -6026.873558
EM: Round [33] log likelihood: -6026.730338
EM: Round [34] log likelihood: -6026.591053
EM: Round [35] log likelihood: -6026.455585
EM: Round [36] log likelihood: -6026.323816
EM: Round [37] log likelihood: -6026.195631
EM: Round [38] log likelihood: -6026.070911
EM: Round [39] log likelihood: -6025.949544
EM: Round [40] log likelihood: -6025.831415
EM: Round [41] log likelihood: -6025.716413
EM: Round [42] log likelihood: -6025.604431
EM: Round [43] log likelihood: -6025.495361
EM: Round [44] log likelihood: -6025.389099
EM: Round [45] log likelihood: -6025.285545
EM: Round [46] log likelihood: -6025.184600
EM: Round [47] log likelihood: -6025.086170
EM: Round [48] log likelihood: -6024.990163
EM: Round [49] log likelihood: -6024.896489
EM: Round [50] log likelihood: -6024.805064
EM: Round [51] log likelihood: -6024.715804
EM: Round [52] log likelihood: -6024.628630
EM: Round [53] log likelihood: -6024.543465
EM: Round [54] log likelihood: -6024.460236
EM: Round [55] log likelihood: -6024.378874
EM: Round [56] log likelihood: -6024.299309
EM: Round [57] log likelihood: -6024.221477
EM: Round [58] log likelihood: -6024.145316
EM: Round [59] log likelihood: -6024.070768
EM: Round [60] log likelihood: -6023.997774
EM: Round [61] log likelihood: -6023.926280
EM: Round [62] log likelihood: -6023.856235
EM: Round [63] log likelihood: -6023.787589
EM: Round [64] log likelihood: -6023.720294
EM: Round [65] log likelihood: -6023.654306
EM: Round [66] log likelihood: -6023.589579
EM: Round [67] log likelihood: -6023.526074
EM: Round [68] log likelihood: -6023.463750
EM: Round [69] log likelihood: -6023.402571
EM: Round [70] log likelihood: -6023.342498
EM: Round [71] log likelihood: -6023.283499
EM: Round [72] log likelihood: -6023.225540
EM: Round [73] log likelihood: -6023.168590
EM: Round [74] log likelihood: -6023.112618
EM: Round [75] log likelihood: -6023.057596
EM: Round [76] log likelihood: -6023.003495
EM: Round [77] log likelihood: -6022.950291
EM: Round [78] log likelihood: -6022.897957
EM: Round [79] log likelihood: -6022.846470
EM: Round [80] log likelihood: -6022.795806
EM: Round [81] log likelihood: -6022.745943
EM: Round [82] log likelihood: -6022.696860
EM: Round [83] log likelihood: -6022.648536
EM: Round [84] log likelihood: -6022.600953
EM: Round [85] log likelihood: -6022.554091
EM: Round [86] log likelihood: -6022.507932
EM: Round [87] log likelihood: -6022.462459
EM: Round [88] log likelihood: -6022.417656
EM: Round [89] log likelihood: -6022.373506
EM: Round [90] log likelihood: -6022.329995
EM: Round [91] log likelihood: -6022.287107
EM: Round [92] log likelihood: -6022.244828
EM: Round [93] log likelihood: -6022.203145
EM: Round [94] log likelihood: -6022.162044
EM: Round [95] log likelihood: -6022.121513
EM: Round [96] log likelihood: -6022.081539
EM: Round [97] log likelihood: -6022.042110
EM: Round [98] log likelihood: -6022.003216
EM: Round [99] log likelihood: -6021.964844
EM: Round [100] log likelihood: -6021.926985
EM: Round [101] log likelihood: -6021.889628
EM: Round [102] log likelihood: -6021.852763
EM: Round [103] log likelihood: -6021.816380
EM: Round [104] log likelihood: -6021.780470
EM: Round [105] log likelihood: -6021.745024
EM: Round [106] log likelihood: -6021.710033
EM: Round [107] log likelihood: -6021.675488
EM: Round [108] log likelihood: -6021.641381
EM: Round [109] log likelihood: -6021.607705
EM: Round [110] log likelihood: -6021.574451
EM: Round [111] log likelihood: -6021.541611
EM: Round [112] log likelihood: -6021.509179
EM: Round [113] log likelihood: -6021.477147
EM: Round [114] log likelihood: -6021.445508
EM: Round [115] log likelihood: -6021.414255
EM: Round [116] log likelihood: -6021.383382
EM: Round [117] log likelihood: -6021.352882
EM: Round [118] log likelihood: -6021.322749
EM: Round [119] log likelihood: -6021.292977
EM: Round [120] log likelihood: -6021.263560
EM: Round [121] log likelihood: -6021.234492
EM: Round [122] log likelihood: -6021.205767
EM: Round [123] log likelihood: -6021.177380
EM: Round [124] log likelihood: -6021.149325
EM: Round [125] log likelihood: -6021.121598
EM: Round [126] log likelihood: -6021.094192
EM: Round [127] log likelihood: -6021.067103
EM: Round [128] log likelihood: -6021.040326
EM: Round [129] log likelihood: -6021.013856
EM: Round [130] log likelihood: -6020.987689
EM: Round [131] log likelihood: -6020.961819
EM: Round [132] log likelihood: -6020.936243
EM: Round [133] log likelihood: -6020.910955
EM: Round [134] log likelihood: -6020.885952
EM: Round [135] log likelihood: -6020.861230
EM: Round [136] log likelihood: -6020.836783
EM: Round [137] log likelihood: -6020.812609
EM: Round [138] log likelihood: -6020.788703
EM: Round [139] log likelihood: -6020.765060
EM: Round [140] log likelihood: -6020.741679
EM: Round [141] log likelihood: -6020.718554
EM: Round [142] log likelihood: -6020.695682
EM: Round [143] log likelihood: -6020.673059
EM: Round [144] log likelihood: -6020.650682
EM: Round [145] log likelihood: -6020.628548
EM: Round [146] log likelihood: -6020.606652
EM: Round [147] log likelihood: -6020.584993
EM: Round [148] log likelihood: -6020.563566
EM: Round [149] log likelihood: -6020.542367
EM: Round [150] log likelihood: -6020.521395
EM: Round [151] log likelihood: -6020.500646
EM: Round [152] log likelihood: -6020.480117
EM: Round [153] log likelihood: -6020.459805
EM: Round [154] log likelihood: -6020.439707
EM: Round [155] log likelihood: -6020.419820
EM: Round [156] log likelihood: -6020.400141
EM: Round [157] log likelihood: -6020.380668
EM: Round [158] log likelihood: -6020.361398
EM: Round [159] log likelihood: -6020.342327
EM: Round [160] log likelihood: -6020.323455
EM: Round [161] log likelihood: -6020.304777
EM: Round [162] log likelihood: -6020.286292
EM: Round [163] log likelihood: -6020.267996
EM: Round [164] log likelihood: -6020.249888
EM: Round [165] log likelihood: -6020.231965
EM: Round [166] log likelihood: -6020.214225
EM: Round [167] log likelihood: -6020.196664
EM: Round [168] log likelihood: -6020.179282
EM: Round [169] log likelihood: -6020.162076
EM: Round [170] log likelihood: -6020.145043
EM: Round [171] log likelihood: -6020.128181
EM: Round [172] log likelihood: -6020.111489
EM: Round [173] log likelihood: -6020.094963
EM: Round [174] log likelihood: -6020.078603
EM: Round [175] log likelihood: -6020.062405
EM: Round [176] log likelihood: -6020.046369
EM: Round [177] log likelihood: -6020.030491
EM: Round [178] log likelihood: -6020.014770
EM: Round [179] log likelihood: -6019.999204
EM: Round [180] log likelihood: -6019.983792
EM: Round [181] log likelihood: -6019.968530
EM: Round [182] log likelihood: -6019.953418
EM: Round [183] log likelihood: -6019.938454
EM: Round [184] log likelihood: -6019.923635
EM: Round [185] log likelihood: -6019.908960
EM: Round [186] log likelihood: -6019.894428
EM: Round [187] log likelihood: -6019.880037
EM: Round [188] log likelihood: -6019.865784
EM: Round [189] log likelihood: -6019.851669
EM: Round [190] log likelihood: -6019.837689
EM: Round [191] log likelihood: -6019.823843
EM: Round [192] log likelihood: -6019.810130
EM: Round [193] log likelihood: -6019.796548
EM: Round [194] log likelihood: -6019.783095
EM: Round [195] log likelihood: -6019.769770
EM: Round [196] log likelihood: -6019.756572
EM: Round [197] log likelihood: -6019.743498
EM: Round [198] log likelihood: -6019.730548
EM: Round [199] log likelihood: -6019.717720
EM: Round [200] log likelihood: -6019.705013
EM: Round [201] log likelihood: -6019.692425
EM: Round [202] log likelihood: -6019.679955
EM: Round [203] log likelihood: -6019.667601
EM: Round [204] log likelihood: -6019.655363
EM: Round [205] log likelihood: -6019.643238
EM: Round [206] log likelihood: -6019.631226
EM: Round [207] log likelihood: -6019.619326
EM: Round [208] log likelihood: -6019.607535
EM: Round [209] log likelihood: -6019.595854
EM: Round [210] log likelihood: -6019.584280
EM: Round [211] log likelihood: -6019.572812
EM: Round [212] log likelihood: -6019.561450
EM: Round [213] log likelihood: -6019.550192
EM: Round [214] log likelihood: -6019.539037
EM: Round [215] log likelihood: -6019.527984
EM: Round [216] log likelihood: -6019.517031
EM: Round [217] log likelihood: -6019.506178
EM: Round [218] log likelihood: -6019.495423
EM: Round [219] log likelihood: -6019.484766
EM: Round [220] log likelihood: -6019.474205
EM: Round [221] log likelihood: -6019.463739
EM: Round [222] log likelihood: -6019.453368
EM: Round [223] log likelihood: -6019.443089
EM: Round [224] log likelihood: -6019.432903
EM: Round [225] log likelihood: -6019.422809
EM: Round [226] log likelihood: -6019.412804
EM: Round [227] log likelihood: -6019.402889
EM: Round [228] log likelihood: -6019.393062
EM: Round [229] log likelihood: -6019.383322
EM: Round [230] log likelihood: -6019.373669
EM: Round [231] log likelihood: -6019.364101
EM: Round [232] log likelihood: -6019.354618
EM: Round [233] log likelihood: -6019.345219
EM: Round [234] log likelihood: -6019.335902
EM: Round [235] log likelihood: -6019.326668
EM: Round [236] log likelihood: -6019.317514
EM: Round [237] log likelihood: -6019.308441
EM: Round [238] log likelihood: -6019.299447
EM: Round [239] log likelihood: -6019.290532
EM: Round [240] log likelihood: -6019.281695
EM: Round [241] log likelihood: -6019.272934
EM: Round [242] log likelihood: -6019.264250
EM: Round [243] log likelihood: -6019.255641
EM: Round [244] log likelihood: -6019.247107
EM: Round [245] log likelihood: -6019.238646
EM: Round [246] log likelihood: -6019.230258
EM: Round [247] log likelihood: -6019.221943
EM: Round [248] log likelihood: -6019.213700
EM: Round [249] log likelihood: -6019.205527
EM: Round [250] log likelihood: -6019.197424
EM: Round [251] log likelihood: -6019.189391
EM: Round [252] log likelihood: -6019.181426
EM: Round [253] log likelihood: -6019.173530
EM: Round [254] log likelihood: -6019.165701
EM: Round [255] log likelihood: -6019.157938
EM: Round [256] log likelihood: -6019.150241
EM: Round [257] log likelihood: -6019.142610
EM: Round [258] log likelihood: -6019.135043
EM: Round [259] log likelihood: -6019.127541
EM: Round [260] log likelihood: -6019.120102
EM: Round [261] log likelihood: -6019.112725
EM: Round [262] log likelihood: -6019.105411
EM: Round [263] log likelihood: -6019.098158
EM: Round [264] log likelihood: -6019.090966
EM: Round [265] log likelihood: -6019.083834
EM: Round [266] log likelihood: -6019.076762
EM: Round [267] log likelihood: -6019.069749
EM: Round [268] log likelihood: -6019.062795
EM: Round [269] log likelihood: -6019.055898
EM: Round [270] log likelihood: -6019.049059
EM: Round [271] log likelihood: -6019.042277
EM: Round [272] log likelihood: -6019.035551
EM: Round [273] log likelihood: -6019.028881
EM: Round [274] log likelihood: -6019.022266
EM: Round [275] log likelihood: -6019.015706
EM: Round [276] log likelihood: -6019.009200
EM: Round [277] log likelihood: -6019.002747
EM: Round [278] log likelihood: -6018.996347
EM: Round [279] log likelihood: -6018.990001
EM: Round [280] log likelihood: -6018.983706
EM: Round [281] log likelihood: -6018.977463
EM: Round [282] log likelihood: -6018.971270
EM: Round [283] log likelihood: -6018.965129
EM: Round [284] log likelihood: -6018.959037
EM: Round [285] log likelihood: -6018.952996
EM: Round [286] log likelihood: -6018.947003
EM: Round [287] log likelihood: -6018.941059
EM: Round [288] log likelihood: -6018.935163
EM: Round [289] log likelihood: -6018.929316
EM: Round [290] log likelihood: -6018.923515
EM: Round [291] log likelihood: -6018.917761
EM: Round [292] log likelihood: -6018.912054
EM: Round [293] log likelihood: -6018.906393
EM: Round [294] log likelihood: -6018.900778
EM: Round [295] log likelihood: -6018.895207
EM: Round [296] log likelihood: -6018.889682
EM: Round [297] log likelihood: -6018.884200
EM: Round [298] log likelihood: -6018.878763
EM: Round [299] log likelihood: -6018.873369
EM: Round [300] log likelihood: -6018.868019
EM: Round [301] log likelihood: -6018.862711
EM: Round [302] log likelihood: -6018.857445
EM: Round [303] log likelihood: -6018.852221
EM: Round [304] log likelihood: -6018.847039
EM: Round [305] log likelihood: -6018.841898
EM: Round [306] log likelihood: -6018.836798
EM: Round [307] log likelihood: -6018.831738
EM: Round [308] log likelihood: -6018.826718
EM: Round [309] log likelihood: -6018.821738
EM: Round [310] log likelihood: -6018.816798
EM: Round [311] log likelihood: -6018.811896
EM: Round [312] log likelihood: -6018.807033
EM: Round [313] log likelihood: -6018.802208
EM: Round [314] log likelihood: -6018.797421
EM: Round [315] log likelihood: -6018.792672
EM: Round [316] log likelihood: -6018.787960
EM: Round [317] log likelihood: -6018.783285
EM: Round [318] log likelihood: -6018.778646
EM: Round [319] log likelihood: -6018.774044
EM: Round [320] log likelihood: -6018.769477
EM: Round [321] log likelihood: -6018.764947
EM: Round [322] log likelihood: -6018.760451
EM: Round [323] log likelihood: -6018.755991
EM: Round [324] log likelihood: -6018.751565
EM: Round [325] log likelihood: -6018.747173
EM: Round [326] log likelihood: -6018.742816
EM: Round [327] log likelihood: -6018.738492
EM: Round [328] log likelihood: -6018.734202
EM: Round [329] log likelihood: -6018.729945
EM: Round [330] log likelihood: -6018.725721
EM: Round [331] log likelihood: -6018.721529
EM: Round [332] log likelihood: -6018.717370
EM: Round [333] log likelihood: -6018.713243
EM: Round [334] log likelihood: -6018.709147
EM: Round [335] log likelihood: -6018.705083
EM: Round [336] log likelihood: -6018.701051
EM: Round [337] log likelihood: -6018.697049
EM: Round [338] log likelihood: -6018.693077
EM: Round [339] log likelihood: -6018.689137
EM: Round [340] log likelihood: -6018.685226
EM: Round [341] log likelihood: -6018.681345
EM: Round [342] log likelihood: -6018.677494
EM: Round [343] log likelihood: -6018.673672
EM: Round [344] log likelihood: -6018.669879
EM: Round [345] log likelihood: -6018.666115
EM: Round [346] log likelihood: -6018.662379
EM: Round [347] log likelihood: -6018.658672
EM: Round [348] log likelihood: -6018.654993
EM: Round [349] log likelihood: -6018.651342
EM: Round [350] log likelihood: -6018.647719
EM: Round [351] log likelihood: -6018.644123
EM: Round [352] log likelihood: -6018.640554
EM: Round [353] log likelihood: -6018.637012
EM: Round [354] log likelihood: -6018.633497
EM: Round [355] log likelihood: -6018.630008
EM: Round [356] log likelihood: -6018.626545
EM: Round [357] log likelihood: -6018.623109
EM: Round [358] log likelihood: -6018.619698
EM: Round [359] log likelihood: -6018.616313
EM: Round [360] log likelihood: -6018.612953
EM: Round [361] log likelihood: -6018.609619
EM: Round [362] log likelihood: -6018.606309
EM: Round [363] log likelihood: -6018.603025
EM: Round [364] log likelihood: -6018.599764
EM: Round [365] log likelihood: -6018.596528
EM: Round [366] log likelihood: -6018.593316
EM: Round [367] log likelihood: -6018.590129
EM: Round [368] log likelihood: -6018.586964
EM: Round [369] log likelihood: -6018.583824
EM: Round [370] log likelihood: -6018.580707
EM: Round [371] log likelihood: -6018.577612
EM: Round [372] log likelihood: -6018.574541
EM: Round [373] log likelihood: -6018.571493
EM: Round [374] log likelihood: -6018.568467
EM: Round [375] log likelihood: -6018.565464
EM: Round [376] log likelihood: -6018.562482
EM: Round [377] log likelihood: -6018.559523
EM: Round [378] log likelihood: -6018.556586
EM: Round [379] log likelihood: -6018.553670
EM: Round [380] log likelihood: -6018.550776
EM: Round [381] log likelihood: -6018.547903
EM: Round [382] log likelihood: -6018.545051
EM: Round [383] log likelihood: -6018.542220
EM: Round [384] log likelihood: -6018.539410
EM: Round [385] log likelihood: -6018.536621
EM: Round [386] log likelihood: -6018.533852
EM: Round [387] log likelihood: -6018.531103
EM: Round [388] log likelihood: -6018.528375
EM: Round [389] log likelihood: -6018.525666
EM: Round [390] log likelihood: -6018.522977
EM: Round [391] log likelihood: -6018.520308
EM: Round [392] log likelihood: -6018.517659
EM: Round [393] log likelihood: -6018.515028
EM: Round [394] log likelihood: -6018.512417
EM: Round [395] log likelihood: -6018.509825
EM: Round [396] log likelihood: -6018.507252
EM: Round [397] log likelihood: -6018.504697
EM: Round [398] log likelihood: -6018.502161
EM: Round [399] log likelihood: -6018.499644
EM: Round [400] log likelihood: -6018.497144
EM: Round [401] log likelihood: -6018.494663
EM: Round [402] log likelihood: -6018.492200
EM: Round [403] log likelihood: -6018.489754
EM: Round [404] log likelihood: -6018.487327
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EM: Round [862] log likelihood: -6018.149784
EM: Round [863] log likelihood: -6018.149664
EM: Round [864] log likelihood: -6018.149544
EM: Round [865] log likelihood: -6018.149425
EM: Round [866] log likelihood: -6018.149307
EM: Round [867] log likelihood: -6018.149190
EM: Round [868] log likelihood: -6018.149073
EM: Round [869] log likelihood: -6018.148957
EM: Round [870] log likelihood: -6018.148842
EM: Round [871] log likelihood: -6018.148727
EM: Round [872] log likelihood: -6018.148613
EM: Round [873] log likelihood: -6018.148500
EM: Round [874] log likelihood: -6018.148387
EM: Round [875] log likelihood: -6018.148275
EM: Round [876] log likelihood: -6018.148164
EM: Round [877] log likelihood: -6018.148054
EM: Round [878] log likelihood: -6018.147944
EM: Round [879] log likelihood: -6018.147835
EM: Round [880] log likelihood: -6018.147726
EM: Round [881] log likelihood: -6018.147618
EM: Round [882] log likelihood: -6018.147511
EM: Round [883] log likelihood: -6018.147404
EM: Round [884] log likelihood: -6018.147298
EM: Round [885] log likelihood: -6018.147193
EM: Round [886] log likelihood: -6018.147088
EM: Round [887] log likelihood: -6018.146984
EM: Round [888] log likelihood: -6018.146881
EM: Round [889] log likelihood: -6018.146778
EM: Round [890] log likelihood: -6018.146676
EM: Round [891] log likelihood: -6018.146574
EM: Round [892] log likelihood: -6018.146473
EM: Round [893] log likelihood: -6018.146373
EM: Round [894] log likelihood: -6018.146273
EM: Stopping iterations at round 894 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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir
-done, see /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3926.358573
EM: Round [1] log likelihood: -3926.270518
EM: Round [2] log likelihood: -3926.268251
EM: Round [3] log likelihood: -3926.268193
EM: Stopping iterations at round 3 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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 246755598
Execution Time = 4.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.LWz6SM2kxe/fi_workdir/microH.dat
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.LWz6SM2kxe/fi_workdir/microH.dat /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/fi_workdir/microH.dat /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LWz6SM2kxe --json_outfile /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LWz6SM2kxe --json_outfile /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000185596.16]
WARNING, no entry stored in dbm for [ENSG00000233806.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.LWz6SM2kxe/ctat_genome_lib_build_dir > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.LWz6SM2kxe/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory