Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/fead9c10c47bacfabd13e68a928eb1/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3d7ee2b28f1612993d80273cf66a27/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3d7ee2b28f1612993d80273cf66a27/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/fead9c10c47bacfabd13e68a928eb1/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/7daadbf5b907f622d438afd404616f/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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 aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 03 20:23:28 ..... started STAR run
Jun 03 20:23:28 ..... loading genome
Jun 03 20:25:12 ... generating Suffix Array index
Jun 03 20:28:58 ... completed Suffix Array index
Jun 03 20:28:58 ..... processing annotations GTF
Jun 03 20:28:59 ..... inserting junctions into the genome indices
Jun 03 20:30:00 ..... started mapping
Jun 03 20:59:58 ..... finished mapping
Jun 03 20:59:59 ..... started sorting BAM
Jun 03 21:00:01 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 36.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
21:00:27 : INFO : Done.
Execution Time = 0.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[4120000] -done parsing /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 189,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 70,
'excessive soft clipping' => 24159,
'per_id < 96' => 14320,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 348,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 24,
'num genes matched < 2' => 75,
'small anchor length' => 17,
'exons hit < 2' => 13,
' ** passed ** ' => 8539,
'seq-similar region overlap' => 299,
'low complexity anchor region' => 43,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 36,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6
};
-writing fusion junction support info.
Execution Time = 2.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[4000] -fusion SPANNING read extraction for scaff: AC242842.2--KCNN3
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[93000] -fusion SPANNING read extraction for scaff: AGO2--TRAPPC9
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[11000] -fusion SPANNING read extraction for scaff: BCAS3--CASC17
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[594000] -fusion SPANNING read extraction for scaff: BRD4--NOTCH3
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[32000] -fusion SPANNING read extraction for scaff: C1orf112--F5
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[43000] -fusion SPANNING read extraction for scaff: CERCAM--VDAC3
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[34000] -fusion SPANNING read extraction for scaff: CERCAM--SLC20A2
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[42000] -fusion SPANNING read extraction for scaff: CNPPD1--GAPDHP49
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[27000] -fusion SPANNING read extraction for scaff: ELK1--SYN1
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[34000] -fusion SPANNING read extraction for scaff: FBXL20--PAMR1
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[30000] -fusion SPANNING read extraction for scaff: FBXL20--SH3RF3
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[297000] -fusion SPANNING read extraction for scaff: GSK3A--CIC
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[26000] -fusion SPANNING read extraction for scaff: IGF1R--TRIM37
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[2000] -fusion SPANNING read extraction for scaff: ING5--FP236383.3
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[77000] -fusion SPANNING read extraction for scaff: INPPL1--GHSR
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[89000] -fusion SPANNING read extraction for scaff: INPPL1--TNFSF10
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[21000] -fusion SPANNING read extraction for scaff: INTS10--AC018541.1
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[23000] -fusion SPANNING read extraction for scaff: INTS2--BCAS3
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[9000] -fusion SPANNING read extraction for scaff: INTS9--DLGAP2
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[2000] -fusion SPANNING read extraction for scaff: LINC00937--AC083906.5
[1000] -fusion SPANNING read extraction for scaff: LINC00937--AC083906.2
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[36000] -fusion SPANNING read extraction for scaff: MAD1L1--SDK1
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[35000] -fusion SPANNING read extraction for scaff: MARK2--AC019211.1
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[23000] -fusion SPANNING read extraction for scaff: NEK6--AC092958.4
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[23000] -fusion SPANNING read extraction for scaff: NEK8--EPHA6
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[97000] -fusion SPANNING read extraction for scaff: NF1--AL353742.1
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[97000] -fusion SPANNING read extraction for scaff: NF1--AL669983.1
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[45000] -fusion SPANNING read extraction for scaff: PARG--BMS1
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[19000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[18000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[15000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[16000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[18000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[43000] -fusion SPANNING read extraction for scaff: PHF21A--KIT
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[15000] -fusion SPANNING read extraction for scaff: PSMD14--AC005040.2
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[15000] -fusion SPANNING read extraction for scaff: PSMD14--LINC01789
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[118000] -fusion SPANNING read extraction for scaff: PTK2--AGO2
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[232000] -fusion SPANNING read extraction for scaff: PTPRF--AC099671.1
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[79000] -fusion SPANNING read extraction for scaff: QKI--AL449043.2
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[109000] -fusion SPANNING read extraction for scaff: QKI--WASHC1
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[30000] -fusion SPANNING read extraction for scaff: RFC1--WDR19
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[5000] -fusion SPANNING read extraction for scaff: RSRC1--IL12A-AS1
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[57000] -fusion SPANNING read extraction for scaff: SCARB1--DHX37
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[91000] -fusion SPANNING read extraction for scaff: SDHA--PLEKHG4B
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[31000] -fusion SPANNING read extraction for scaff: SRP68--ZMAT3
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[71000] -fusion SPANNING read extraction for scaff: TBC1D8--AGFG1
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[22000] -fusion SPANNING read extraction for scaff: TERF1--KCNB2
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[46000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[15000] -fusion SPANNING read extraction for scaff: TRIM37--AC022523.1
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[11000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[27000] -fusion SPANNING read extraction for scaff: USP37--AC008281.1
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[27000] -fusion SPANNING read extraction for scaff: USP37--AC009310.1
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[23000] -fusion SPANNING read extraction for scaff: UXS1--NHEJ1
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[31000] -fusion SPANNING read extraction for scaff: VMP1--PINX1
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[38000] -fusion SPANNING read extraction for scaff: VPS72--AC137761.1
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[28000] -fusion SPANNING read extraction for scaff: WT1--AC006504.5
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[27000] -fusion SPANNING read extraction for scaff: WT1--AC006504.2
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[27000] -fusion SPANNING read extraction for scaff: WT1--AC005357.2
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[190000] -fusion SPANNING read extraction for scaff: XPO1--USP34
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[13000] -fusion SPANNING read extraction for scaff: ZFP3--TM4SF5
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[7000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
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[9000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 32227,
'lacks exon overlap' => 58169
};
Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -15391.992536
EM: Round [1] log likelihood: -15386.108100
EM: Round [2] log likelihood: -15385.060296
EM: Round [3] log likelihood: -15384.181845
EM: Round [4] log likelihood: -15383.427892
EM: Round [5] log likelihood: -15382.775760
EM: Round [6] log likelihood: -15382.207868
EM: Round [7] log likelihood: -15381.710317
EM: Round [8] log likelihood: -15381.271962
EM: Round [9] log likelihood: -15380.883760
EM: Round [10] log likelihood: -15380.538305
EM: Round [11] log likelihood: -15380.229472
EM: Round [12] log likelihood: -15379.952166
EM: Round [13] log likelihood: -15379.702117
EM: Round [14] log likelihood: -15379.475729
EM: Round [15] log likelihood: -15379.269959
EM: Round [16] log likelihood: -15379.082219
EM: Round [17] log likelihood: -15378.910303
EM: Round [18] log likelihood: -15378.752320
EM: Round [19] log likelihood: -15378.606649
EM: Round [20] log likelihood: -15378.471890
EM: Round [21] log likelihood: -15378.346837
EM: Round [22] log likelihood: -15378.230444
EM: Round [23] log likelihood: -15378.121804
EM: Round [24] log likelihood: -15378.020126
EM: Round [25] log likelihood: -15377.924723
EM: Round [26] log likelihood: -15377.834990
EM: Round [27] log likelihood: -15377.750402
EM: Round [28] log likelihood: -15377.670494
EM: Round [29] log likelihood: -15377.594858
EM: Round [30] log likelihood: -15377.523133
EM: Round [31] log likelihood: -15377.455001
EM: Round [32] log likelihood: -15377.390179
EM: Round [33] log likelihood: -15377.328414
EM: Round [34] log likelihood: -15377.269482
EM: Round [35] log likelihood: -15377.213184
EM: Round [36] log likelihood: -15377.159337
EM: Round [37] log likelihood: -15377.107781
EM: Round [38] log likelihood: -15377.058369
EM: Round [39] log likelihood: -15377.010969
EM: Round [40] log likelihood: -15376.965461
EM: Round [41] log likelihood: -15376.921736
EM: Round [42] log likelihood: -15376.879695
EM: Round [43] log likelihood: -15376.839245
EM: Round [44] log likelihood: -15376.800304
EM: Round [45] log likelihood: -15376.762794
EM: Round [46] log likelihood: -15376.726645
EM: Round [47] log likelihood: -15376.691790
EM: Round [48] log likelihood: -15376.658169
EM: Round [49] log likelihood: -15376.625724
EM: Round [50] log likelihood: -15376.594403
EM: Round [51] log likelihood: -15376.564157
EM: Round [52] log likelihood: -15376.534938
EM: Round [53] log likelihood: -15376.506704
EM: Round [54] log likelihood: -15376.479413
EM: Round [55] log likelihood: -15376.453028
EM: Round [56] log likelihood: -15376.427511
EM: Round [57] log likelihood: -15376.402829
EM: Round [58] log likelihood: -15376.378948
EM: Round [59] log likelihood: -15376.355838
EM: Round [60] log likelihood: -15376.333470
EM: Round [61] log likelihood: -15376.311816
EM: Round [62] log likelihood: -15376.290849
EM: Round [63] log likelihood: -15376.270544
EM: Round [64] log likelihood: -15376.250876
EM: Round [65] log likelihood: -15376.231824
EM: Round [66] log likelihood: -15376.213364
EM: Round [67] log likelihood: -15376.195477
EM: Round [68] log likelihood: -15376.178141
EM: Round [69] log likelihood: -15376.161337
EM: Round [70] log likelihood: -15376.145047
EM: Round [71] log likelihood: -15376.129254
EM: Round [72] log likelihood: -15376.113940
EM: Round [73] log likelihood: -15376.099088
EM: Round [74] log likelihood: -15376.084684
EM: Round [75] log likelihood: -15376.070712
EM: Round [76] log likelihood: -15376.057157
EM: Round [77] log likelihood: -15376.044007
EM: Round [78] log likelihood: -15376.031246
EM: Round [79] log likelihood: -15376.018863
EM: Round [80] log likelihood: -15376.006845
EM: Round [81] log likelihood: -15375.995179
EM: Round [82] log likelihood: -15375.983856
EM: Round [83] log likelihood: -15375.972862
EM: Round [84] log likelihood: -15375.962188
EM: Round [85] log likelihood: -15375.951824
EM: Round [86] log likelihood: -15375.941758
EM: Round [87] log likelihood: -15375.931983
EM: Round [88] log likelihood: -15375.922488
EM: Round [89] log likelihood: -15375.913264
EM: Round [90] log likelihood: -15375.904304
EM: Round [91] log likelihood: -15375.895598
EM: Round [92] log likelihood: -15375.887138
EM: Round [93] log likelihood: -15375.878918
EM: Round [94] log likelihood: -15375.870928
EM: Round [95] log likelihood: -15375.863163
EM: Round [96] log likelihood: -15375.855615
EM: Round [97] log likelihood: -15375.848276
EM: Round [98] log likelihood: -15375.841142
EM: Round [99] log likelihood: -15375.834205
EM: Round [100] log likelihood: -15375.827460
EM: Round [101] log likelihood: -15375.820899
EM: Round [102] log likelihood: -15375.814519
EM: Round [103] log likelihood: -15375.808313
EM: Round [104] log likelihood: -15375.802276
EM: Round [105] log likelihood: -15375.796402
EM: Round [106] log likelihood: -15375.790687
EM: Round [107] log likelihood: -15375.785126
EM: Round [108] log likelihood: -15375.779715
EM: Round [109] log likelihood: -15375.774448
EM: Round [110] log likelihood: -15375.769322
EM: Round [111] log likelihood: -15375.764331
EM: Round [112] log likelihood: -15375.759473
EM: Round [113] log likelihood: -15375.754743
EM: Round [114] log likelihood: -15375.750137
EM: Round [115] log likelihood: -15375.745652
EM: Round [116] log likelihood: -15375.741284
EM: Round [117] log likelihood: -15375.737029
EM: Round [118] log likelihood: -15375.732885
EM: Round [119] log likelihood: -15375.728847
EM: Round [120] log likelihood: -15375.724914
EM: Round [121] log likelihood: -15375.721081
EM: Round [122] log likelihood: -15375.717346
EM: Round [123] log likelihood: -15375.713705
EM: Round [124] log likelihood: -15375.710157
EM: Round [125] log likelihood: -15375.706698
EM: Round [126] log likelihood: -15375.703326
EM: Round [127] log likelihood: -15375.700039
EM: Round [128] log likelihood: -15375.696833
EM: Round [129] log likelihood: -15375.693707
EM: Round [130] log likelihood: -15375.690658
EM: Round [131] log likelihood: -15375.687684
EM: Round [132] log likelihood: -15375.684783
EM: Round [133] log likelihood: -15375.681953
EM: Round [134] log likelihood: -15375.679192
EM: Round [135] log likelihood: -15375.676497
EM: Round [136] log likelihood: -15375.673867
EM: Round [137] log likelihood: -15375.671301
EM: Round [138] log likelihood: -15375.668796
EM: Round [139] log likelihood: -15375.666350
EM: Round [140] log likelihood: -15375.663962
EM: Round [141] log likelihood: -15375.661631
EM: Round [142] log likelihood: -15375.659354
EM: Round [143] log likelihood: -15375.657130
EM: Round [144] log likelihood: -15375.654958
EM: Round [145] log likelihood: -15375.652836
EM: Round [146] log likelihood: -15375.650764
EM: Round [147] log likelihood: -15375.648738
EM: Round [148] log likelihood: -15375.646759
EM: Round [149] log likelihood: -15375.644825
EM: Round [150] log likelihood: -15375.642935
EM: Round [151] log likelihood: -15375.641087
EM: Round [152] log likelihood: -15375.639280
EM: Round [153] log likelihood: -15375.637514
EM: Round [154] log likelihood: -15375.635787
EM: Round [155] log likelihood: -15375.634098
EM: Round [156] log likelihood: -15375.632446
EM: Round [157] log likelihood: -15375.630830
EM: Round [158] log likelihood: -15375.629250
EM: Round [159] log likelihood: -15375.627703
EM: Round [160] log likelihood: -15375.626190
EM: Round [161] log likelihood: -15375.624709
EM: Round [162] log likelihood: -15375.623260
EM: Round [163] log likelihood: -15375.621841
EM: Round [164] log likelihood: -15375.620452
EM: Round [165] log likelihood: -15375.619092
EM: Round [166] log likelihood: -15375.617761
EM: Round [167] log likelihood: -15375.616457
EM: Round [168] log likelihood: -15375.615181
EM: Round [169] log likelihood: -15375.613930
EM: Round [170] log likelihood: -15375.612705
EM: Round [171] log likelihood: -15375.611505
EM: Round [172] log likelihood: -15375.610329
EM: Round [173] log likelihood: -15375.609177
EM: Round [174] log likelihood: -15375.608047
EM: Round [175] log likelihood: -15375.606940
EM: Round [176] log likelihood: -15375.605855
EM: Round [177] log likelihood: -15375.604792
EM: Round [178] log likelihood: -15375.603749
EM: Round [179] log likelihood: -15375.602726
EM: Round [180] log likelihood: -15375.601723
EM: Round [181] log likelihood: -15375.600740
EM: Round [182] log likelihood: -15375.599775
EM: Round [183] log likelihood: -15375.598828
EM: Round [184] log likelihood: -15375.597900
EM: Round [185] log likelihood: -15375.596989
EM: Round [186] log likelihood: -15375.596095
EM: Round [187] log likelihood: -15375.595217
EM: Round [188] log likelihood: -15375.594356
EM: Round [189] log likelihood: -15375.593510
EM: Round [190] log likelihood: -15375.592680
EM: Round [191] log likelihood: -15375.591866
EM: Round [192] log likelihood: -15375.591065
EM: Round [193] log likelihood: -15375.590280
EM: Round [194] log likelihood: -15375.589508
EM: Round [195] log likelihood: -15375.588750
EM: Round [196] log likelihood: -15375.588005
EM: Round [197] log likelihood: -15375.587273
EM: Round [198] log likelihood: -15375.586555
EM: Round [199] log likelihood: -15375.585848
EM: Round [200] log likelihood: -15375.585154
EM: Round [201] log likelihood: -15375.584472
EM: Round [202] log likelihood: -15375.583801
EM: Round [203] log likelihood: -15375.583142
EM: Round [204] log likelihood: -15375.582494
EM: Round [205] log likelihood: -15375.581857
EM: Round [206] log likelihood: -15375.581230
EM: Round [207] log likelihood: -15375.580614
EM: Round [208] log likelihood: -15375.580008
EM: Round [209] log likelihood: -15375.579412
EM: Round [210] log likelihood: -15375.578826
EM: Round [211] log likelihood: -15375.578249
EM: Round [212] log likelihood: -15375.577682
EM: Round [213] log likelihood: -15375.577124
EM: Round [214] log likelihood: -15375.576574
EM: Round [215] log likelihood: -15375.576033
EM: Round [216] log likelihood: -15375.575501
EM: Round [217] log likelihood: -15375.574978
EM: Round [218] log likelihood: -15375.574462
EM: Round [219] log likelihood: -15375.573954
EM: Round [220] log likelihood: -15375.573455
EM: Round [221] log likelihood: -15375.572963
EM: Round [222] log likelihood: -15375.572478
EM: Round [223] log likelihood: -15375.572001
EM: Round [224] log likelihood: -15375.571531
EM: Round [225] log likelihood: -15375.571068
EM: Round [226] log likelihood: -15375.570612
EM: Round [227] log likelihood: -15375.570163
EM: Round [228] log likelihood: -15375.569721
EM: Round [229] log likelihood: -15375.569285
EM: Round [230] log likelihood: -15375.568856
EM: Round [231] log likelihood: -15375.568432
EM: Round [232] log likelihood: -15375.568015
EM: Round [233] log likelihood: -15375.567604
EM: Round [234] log likelihood: -15375.567199
EM: Round [235] log likelihood: -15375.566800
EM: Round [236] log likelihood: -15375.566406
EM: Round [237] log likelihood: -15375.566018
EM: Round [238] log likelihood: -15375.565636
EM: Round [239] log likelihood: -15375.565259
EM: Round [240] log likelihood: -15375.564887
EM: Round [241] log likelihood: -15375.564520
EM: Round [242] log likelihood: -15375.564158
EM: Round [243] log likelihood: -15375.563802
EM: Round [244] log likelihood: -15375.563450
EM: Round [245] log likelihood: -15375.563103
EM: Round [246] log likelihood: -15375.562761
EM: Round [247] log likelihood: -15375.562423
EM: Round [248] log likelihood: -15375.562090
EM: Round [249] log likelihood: -15375.561762
EM: Round [250] log likelihood: -15375.561438
EM: Round [251] log likelihood: -15375.561118
EM: Round [252] log likelihood: -15375.560802
EM: Round [253] log likelihood: -15375.560491
EM: Round [254] log likelihood: -15375.560183
EM: Round [255] log likelihood: -15375.559880
EM: Round [256] log likelihood: -15375.559581
EM: Round [257] log likelihood: -15375.559285
EM: Round [258] log likelihood: -15375.558994
EM: Round [259] log likelihood: -15375.558706
EM: Round [260] log likelihood: -15375.558422
EM: Round [261] log likelihood: -15375.558141
EM: Round [262] log likelihood: -15375.557864
EM: Round [263] log likelihood: -15375.557591
EM: Round [264] log likelihood: -15375.557321
EM: Round [265] log likelihood: -15375.557054
EM: Round [266] log likelihood: -15375.556791
EM: Round [267] log likelihood: -15375.556531
EM: Round [268] log likelihood: -15375.556274
EM: Round [269] log likelihood: -15375.556021
EM: Round [270] log likelihood: -15375.555771
EM: Round [271] log likelihood: -15375.555523
EM: Round [272] log likelihood: -15375.555279
EM: Round [273] log likelihood: -15375.555038
EM: Round [274] log likelihood: -15375.554800
EM: Round [275] log likelihood: -15375.554564
EM: Round [276] log likelihood: -15375.554332
EM: Round [277] log likelihood: -15375.554102
EM: Round [278] log likelihood: -15375.553875
EM: Round [279] log likelihood: -15375.553651
EM: Round [280] log likelihood: -15375.553429
EM: Round [281] log likelihood: -15375.553211
EM: Round [282] log likelihood: -15375.552994
EM: Round [283] log likelihood: -15375.552781
EM: Round [284] log likelihood: -15375.552569
EM: Round [285] log likelihood: -15375.552361
EM: Round [286] log likelihood: -15375.552155
EM: Round [287] log likelihood: -15375.551951
EM: Round [288] log likelihood: -15375.551749
EM: Round [289] log likelihood: -15375.551550
EM: Round [290] log likelihood: -15375.551354
EM: Round [291] log likelihood: -15375.551159
EM: Round [292] log likelihood: -15375.550967
EM: Round [293] log likelihood: -15375.550777
EM: Round [294] log likelihood: -15375.550589
EM: Round [295] log likelihood: -15375.550404
EM: Round [296] log likelihood: -15375.550220
EM: Round [297] log likelihood: -15375.550039
EM: Round [298] log likelihood: -15375.549860
EM: Round [299] log likelihood: -15375.549682
EM: Round [300] log likelihood: -15375.549507
EM: Round [301] log likelihood: -15375.549334
EM: Round [302] log likelihood: -15375.549163
EM: Round [303] log likelihood: -15375.548993
EM: Round [304] log likelihood: -15375.548826
EM: Round [305] log likelihood: -15375.548660
EM: Round [306] log likelihood: -15375.548497
EM: Round [307] log likelihood: -15375.548335
EM: Round [308] log likelihood: -15375.548175
EM: Round [309] log likelihood: -15375.548017
EM: Round [310] log likelihood: -15375.547860
EM: Round [311] log likelihood: -15375.547705
EM: Round [312] log likelihood: -15375.547552
EM: Round [313] log likelihood: -15375.547401
EM: Round [314] log likelihood: -15375.547251
EM: Round [315] log likelihood: -15375.547103
EM: Round [316] log likelihood: -15375.546957
EM: Round [317] log likelihood: -15375.546812
EM: Round [318] log likelihood: -15375.546669
EM: Round [319] log likelihood: -15375.546527
EM: Round [320] log likelihood: -15375.546387
EM: Round [321] log likelihood: -15375.546249
EM: Round [322] log likelihood: -15375.546112
EM: Round [323] log likelihood: -15375.545976
EM: Round [324] log likelihood: -15375.545842
EM: Round [325] log likelihood: -15375.545709
EM: Round [326] log likelihood: -15375.545578
EM: Round [327] log likelihood: -15375.545449
EM: Round [328] log likelihood: -15375.545320
EM: Round [329] log likelihood: -15375.545193
EM: Round [330] log likelihood: -15375.545068
EM: Round [331] log likelihood: -15375.544943
EM: Round [332] log likelihood: -15375.544820
EM: Round [333] log likelihood: -15375.544699
EM: Round [334] log likelihood: -15375.544579
EM: Round [335] log likelihood: -15375.544459
EM: Round [336] log likelihood: -15375.544342
EM: Round [337] log likelihood: -15375.544225
EM: Round [338] log likelihood: -15375.544110
EM: Round [339] log likelihood: -15375.543996
EM: Round [340] log likelihood: -15375.543883
EM: Round [341] log likelihood: -15375.543772
EM: Round [342] log likelihood: -15375.543661
EM: Round [343] log likelihood: -15375.543552
EM: Round [344] log likelihood: -15375.543444
EM: Round [345] log likelihood: -15375.543337
EM: Round [346] log likelihood: -15375.543231
EM: Round [347] log likelihood: -15375.543126
EM: Round [348] log likelihood: -15375.543023
EM: Round [349] log likelihood: -15375.542920
EM: Round [350] log likelihood: -15375.542819
EM: Round [351] log likelihood: -15375.542718
EM: Round [352] log likelihood: -15375.542619
EM: Stopping iterations at round 352 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir
-done, see /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -13858.419657
EM: Round [1] log likelihood: -13856.576383
EM: Round [2] log likelihood: -13856.560456
EM: Round [3] log likelihood: -13856.560374
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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 154970419
Execution Time = 3.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000234285.1]
WARNING, no entry stored in dbm for [ENSG00000267623.3]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000260158.1]
WARNING, no entry stored in dbm for [ENSG00000260785.2]
WARNING, no entry stored in dbm for [ENSG00000239498.1]
WARNING, no entry stored in dbm for [ENSG00000285409.1]
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 [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory