Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/00f1f9abf371f5d31efe64f9c62f7f/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusionreport.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/bd9a58555a24a842618f07accd6fc4/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/bd9a58555a24a842618f07accd6fc4/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5b6b38f5f2034cec6042402a189a36/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5b6b38f5f2034cec6042402a189a36/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusionreport.tsv --gtf /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.n5MsjTQPJV/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.n5MsjTQPJV/cytoBand.txt
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed
-parsing GTF file: /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star --out_dir /tmp/nxf.n5MsjTQPJV/fi_workdir --reads "/tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_1.fastp.fastq.gz /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_1.fastp.fastq.gz /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 08:23:41 ..... started STAR run
Jun 08 08:23:41 ..... loading genome
Jun 08 08:25:23 ... generating Suffix Array index
Jun 08 08:29:16 ... completed Suffix Array index
Jun 08 08:29:16 ..... processing annotations GTF
Jun 08 08:29:16 ..... inserting junctions into the genome indices
Jun 08 08:30:17 ..... started mapping
Jun 08 09:00:05 ..... finished mapping
Jun 08 09:00:07 ..... started sorting BAM
Jun 08 09:00:16 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.sortedByCoord.out.bam
Execution Time = 36.78 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n5MsjTQPJV/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star --out_dir /tmp/nxf.n5MsjTQPJV/fi_workdir --reads "/tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_1.fastp.fastq.gz /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --remove_dups
09:01:35 : INFO : Done.
Execution Time = 1.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.14 minutes. CMD: samtools index /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf
-parsing /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam
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[15860000] -done parsing /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 592,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 28,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 143,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num genes matched < 2' => 54,
'per_id < 96' => 77825,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 101,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
'small anchor length' => 125,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 68,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 8,
' ** passed ** ' => 10269,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 320,
'excessive soft clipping' => 76021,
'exons hit < 2' => 4,
'low complexity anchor region' => 21,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 2
};
-writing fusion junction support info.
Execution Time = 9.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[56000] -fusion SPANNING read extraction for scaff: ELL--AC003973.1
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[61000] -fusion SPANNING read extraction for scaff: ELL--ZNF257
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[7223000] -fusion SPANNING read extraction for scaff: ERBB2--BORCS8
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[127000] -fusion SPANNING read extraction for scaff: PIK3R2--ATP13A1
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[73000] -fusion SPANNING read extraction for scaff: PIK3R2--ZNF101
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[30000] -fusion SPANNING read extraction for scaff: RNF19A--CAMK2A
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[114000] -fusion SPANNING read extraction for scaff: SSH2--KXD1
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[36000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[60000] -fusion SPANNING read extraction for scaff: TAOK1--SLC13A2
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[371000] -fusion SPANNING read extraction for scaff: UPF1--PGAP3
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[138000] -fusion SPANNING read extraction for scaff: ZNF14--NF1
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[23000] -fusion SPANNING read extraction for scaff: ZNF14--ZNF257
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[185000] -fusion SPANNING read extraction for scaff: ZNF208--IKZF3
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 203,
'lacks exon overlap' => 78668
};
Execution Time = 26.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -10800.798104
EM: Round [1] log likelihood: -10762.677124
EM: Round [2] log likelihood: -10755.944417
EM: Round [3] log likelihood: -10754.554535
EM: Round [4] log likelihood: -10754.253001
EM: Round [5] log likelihood: -10754.186614
EM: Round [6] log likelihood: -10754.171936
EM: Round [7] log likelihood: -10754.168687
EM: Round [8] log likelihood: -10754.167968
EM: Round [9] log likelihood: -10754.167808
EM: Round [10] log likelihood: -10754.167773
EM: Stopping iterations at round 10 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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.n5MsjTQPJV/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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5MsjTQPJV/fi_workdir/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam
Execution Time = 0.14 minutes. CMD: samtools index /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam
Running: touch /tmp/nxf.n5MsjTQPJV/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam into /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.read_coords > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n5MsjTQPJV/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.consolidated.bam.frag_coords.coord_sorted