Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/2ebfe6fbd205a39a751dbf01c37fb2/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/bf02b30f5709e60ae56858243e4e69/.command.sh
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/1b/bf02b30f5709e60ae56858243e4e69/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/2ebfe6fbd205a39a751dbf01c37fb2/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/1e49e68bafc2809e9b7e3f93517ff0/aih-tih-sc-98fc22-R1_A23WJ53LT4_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-98fc22-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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-98fc22-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/cytoBand.txt
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.yzUtTbjI1y/fi_workdir --reads "/tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:18:41 ..... started STAR run
Jun 08 10:18:41 ..... loading genome
Jun 08 10:20:24 ... generating Suffix Array index
Jun 08 10:24:25 ... completed Suffix Array index
Jun 08 10:24:25 ..... processing annotations GTF
Jun 08 10:24:25 ..... inserting junctions into the genome indices
Jun 08 10:25:28 ..... started mapping
Jun 08 11:29:30 ..... finished mapping
Jun 08 11:29:32 ..... started sorting BAM
Jun 08 11:29:32 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 70.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.yzUtTbjI1y/fi_workdir --reads "/tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:29:39 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1100000] -done parsing /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 67,
'excessive soft clipping' => 7010,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 354,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 480,
'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 1,
' ** passed ** ' => 3084,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 36,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 10 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'exons hit < 2' => 6,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 30,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 32,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 288,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 238,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
'low complexity anchor region' => 27,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26,
'per_id < 96' => 4409,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 153,
'seq-similar region overlap' => 162,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 8,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 18,
'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 21,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 64,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 396,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 16,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 335,
'num genes matched < 2' => 22,
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 12,
'small anchor length' => 11,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1590,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 812,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 64
};
-writing fusion junction support info.
Execution Time = 0.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[247000] -fusion SPANNING read extraction for scaff: ETV6--POLE
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1
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[15000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13
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[490000] -fusion SPANNING read extraction for scaff: PDXDC2P--NPIPB3
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[34000] -fusion SPANNING read extraction for scaff: SLCO1B3--SLCO1B7
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[85000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[28000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[29000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 27945,
'seq similar region alignment' => 32659
};
Execution Time = 1.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4024.108138
EM: Round [1] log likelihood: -4023.778601
EM: Round [2] log likelihood: -4023.696087
EM: Round [3] log likelihood: -4023.618428
EM: Round [4] log likelihood: -4023.543964
EM: Round [5] log likelihood: -4023.472482
EM: Round [6] log likelihood: -4023.403810
EM: Round [7] log likelihood: -4023.337794
EM: Round [8] log likelihood: -4023.274290
EM: Round [9] log likelihood: -4023.213165
EM: Round [10] log likelihood: -4023.154295
EM: Round [11] log likelihood: -4023.097566
EM: Round [12] log likelihood: -4023.042873
EM: Round [13] log likelihood: -4022.990115
EM: Round [14] log likelihood: -4022.939200
EM: Round [15] log likelihood: -4022.890042
EM: Round [16] log likelihood: -4022.842560
EM: Round [17] log likelihood: -4022.796677
EM: Round [18] log likelihood: -4022.752323
EM: Round [19] log likelihood: -4022.709430
EM: Round [20] log likelihood: -4022.667936
EM: Round [21] log likelihood: -4022.627782
EM: Round [22] log likelihood: -4022.588910
EM: Round [23] log likelihood: -4022.551269
EM: Round [24] log likelihood: -4022.514808
EM: Round [25] log likelihood: -4022.479481
EM: Round [26] log likelihood: -4022.445242
EM: Round [27] log likelihood: -4022.412050
EM: Round [28] log likelihood: -4022.379863
EM: Round [29] log likelihood: -4022.348644
EM: Round [30] log likelihood: -4022.318356
EM: Round [31] log likelihood: -4022.288966
EM: Round [32] log likelihood: -4022.260439
EM: Round [33] log likelihood: -4022.232746
EM: Round [34] log likelihood: -4022.205855
EM: Round [35] log likelihood: -4022.179739
EM: Round [36] log likelihood: -4022.154370
EM: Round [37] log likelihood: -4022.129723
EM: Round [38] log likelihood: -4022.105773
EM: Round [39] log likelihood: -4022.082496
EM: Round [40] log likelihood: -4022.059869
EM: Round [41] log likelihood: -4022.037871
EM: Round [42] log likelihood: -4022.016480
EM: Round [43] log likelihood: -4021.995678
EM: Round [44] log likelihood: -4021.975445
EM: Round [45] log likelihood: -4021.955762
EM: Round [46] log likelihood: -4021.936613
EM: Round [47] log likelihood: -4021.917980
EM: Round [48] log likelihood: -4021.899846
EM: Round [49] log likelihood: -4021.882197
EM: Round [50] log likelihood: -4021.865017
EM: Round [51] log likelihood: -4021.848293
EM: Round [52] log likelihood: -4021.832009
EM: Round [53] log likelihood: -4021.816153
EM: Round [54] log likelihood: -4021.800712
EM: Round [55] log likelihood: -4021.785674
EM: Round [56] log likelihood: -4021.771026
EM: Round [57] log likelihood: -4021.756757
EM: Round [58] log likelihood: -4021.742856
EM: Round [59] log likelihood: -4021.729312
EM: Round [60] log likelihood: -4021.716115
EM: Round [61] log likelihood: -4021.703255
EM: Round [62] log likelihood: -4021.690723
EM: Round [63] log likelihood: -4021.678508
EM: Round [64] log likelihood: -4021.666602
EM: Round [65] log likelihood: -4021.654996
EM: Round [66] log likelihood: -4021.643682
EM: Round [67] log likelihood: -4021.632652
EM: Round [68] log likelihood: -4021.621898
EM: Round [69] log likelihood: -4021.611412
EM: Round [70] log likelihood: -4021.601186
EM: Round [71] log likelihood: -4021.591215
EM: Round [72] log likelihood: -4021.581490
EM: Round [73] log likelihood: -4021.572006
EM: Round [74] log likelihood: -4021.562755
EM: Round [75] log likelihood: -4021.553731
EM: Round [76] log likelihood: -4021.544929
EM: Round [77] log likelihood: -4021.536342
EM: Round [78] log likelihood: -4021.527965
EM: Round [79] log likelihood: -4021.519792
EM: Round [80] log likelihood: -4021.511818
EM: Round [81] log likelihood: -4021.504037
EM: Round [82] log likelihood: -4021.496445
EM: Round [83] log likelihood: -4021.489036
EM: Round [84] log likelihood: -4021.481806
EM: Round [85] log likelihood: -4021.474751
EM: Round [86] log likelihood: -4021.467865
EM: Round [87] log likelihood: -4021.461144
EM: Round [88] log likelihood: -4021.454585
EM: Round [89] log likelihood: -4021.448182
EM: Round [90] log likelihood: -4021.441933
EM: Round [91] log likelihood: -4021.435832
EM: Round [92] log likelihood: -4021.429877
EM: Round [93] log likelihood: -4021.424063
EM: Round [94] log likelihood: -4021.418388
EM: Round [95] log likelihood: -4021.412847
EM: Round [96] log likelihood: -4021.407438
EM: Round [97] log likelihood: -4021.402156
EM: Round [98] log likelihood: -4021.396999
EM: Round [99] log likelihood: -4021.391964
EM: Round [100] log likelihood: -4021.387048
EM: Round [101] log likelihood: -4021.382247
EM: Round [102] log likelihood: -4021.377559
EM: Round [103] log likelihood: -4021.372981
EM: Round [104] log likelihood: -4021.368510
EM: Round [105] log likelihood: -4021.364145
EM: Round [106] log likelihood: -4021.359881
EM: Round [107] log likelihood: -4021.355717
EM: Round [108] log likelihood: -4021.351650
EM: Round [109] log likelihood: -4021.347678
EM: Round [110] log likelihood: -4021.343799
EM: Round [111] log likelihood: -4021.340010
EM: Round [112] log likelihood: -4021.336309
EM: Round [113] log likelihood: -4021.332695
EM: Round [114] log likelihood: -4021.329164
EM: Round [115] log likelihood: -4021.325715
EM: Round [116] log likelihood: -4021.322346
EM: Round [117] log likelihood: -4021.319055
EM: Round [118] log likelihood: -4021.315840
EM: Round [119] log likelihood: -4021.312700
EM: Round [120] log likelihood: -4021.309632
EM: Round [121] log likelihood: -4021.306635
EM: Round [122] log likelihood: -4021.303707
EM: Round [123] log likelihood: -4021.300847
EM: Round [124] log likelihood: -4021.298052
EM: Round [125] log likelihood: -4021.295322
EM: Round [126] log likelihood: -4021.292655
EM: Round [127] log likelihood: -4021.290049
EM: Round [128] log likelihood: -4021.287503
EM: Round [129] log likelihood: -4021.285015
EM: Round [130] log likelihood: -4021.282585
EM: Round [131] log likelihood: -4021.280210
EM: Round [132] log likelihood: -4021.277889
EM: Round [133] log likelihood: -4021.275622
EM: Round [134] log likelihood: -4021.273407
EM: Round [135] log likelihood: -4021.271242
EM: Round [136] log likelihood: -4021.269127
EM: Round [137] log likelihood: -4021.267060
EM: Round [138] log likelihood: -4021.265041
EM: Round [139] log likelihood: -4021.263067
EM: Round [140] log likelihood: -4021.261139
EM: Round [141] log likelihood: -4021.259255
EM: Round [142] log likelihood: -4021.257413
EM: Round [143] log likelihood: -4021.255614
EM: Round [144] log likelihood: -4021.253855
EM: Round [145] log likelihood: -4021.252137
EM: Round [146] log likelihood: -4021.250458
EM: Round [147] log likelihood: -4021.248817
EM: Round [148] log likelihood: -4021.247213
EM: Round [149] log likelihood: -4021.245646
EM: Round [150] log likelihood: -4021.244114
EM: Round [151] log likelihood: -4021.242617
EM: Round [152] log likelihood: -4021.241154
EM: Round [153] log likelihood: -4021.239725
EM: Round [154] log likelihood: -4021.238327
EM: Round [155] log likelihood: -4021.236962
EM: Round [156] log likelihood: -4021.235627
EM: Round [157] log likelihood: -4021.234323
EM: Round [158] log likelihood: -4021.233048
EM: Round [159] log likelihood: -4021.231803
EM: Round [160] log likelihood: -4021.230585
EM: Round [161] log likelihood: -4021.229395
EM: Round [162] log likelihood: -4021.228232
EM: Round [163] log likelihood: -4021.227095
EM: Round [164] log likelihood: -4021.225984
EM: Round [165] log likelihood: -4021.224898
EM: Round [166] log likelihood: -4021.223836
EM: Round [167] log likelihood: -4021.222799
EM: Round [168] log likelihood: -4021.221785
EM: Round [169] log likelihood: -4021.220794
EM: Round [170] log likelihood: -4021.219825
EM: Round [171] log likelihood: -4021.218879
EM: Round [172] log likelihood: -4021.217953
EM: Round [173] log likelihood: -4021.217049
EM: Round [174] log likelihood: -4021.216164
EM: Round [175] log likelihood: -4021.215300
EM: Round [176] log likelihood: -4021.214456
EM: Round [177] log likelihood: -4021.213630
EM: Round [178] log likelihood: -4021.212823
EM: Round [179] log likelihood: -4021.212034
EM: Round [180] log likelihood: -4021.211263
EM: Round [181] log likelihood: -4021.210509
EM: Round [182] log likelihood: -4021.209773
EM: Round [183] log likelihood: -4021.209053
EM: Round [184] log likelihood: -4021.208349
EM: Round [185] log likelihood: -4021.207661
EM: Round [186] log likelihood: -4021.206988
EM: Round [187] log likelihood: -4021.206331
EM: Round [188] log likelihood: -4021.205688
EM: Round [189] log likelihood: -4021.205060
EM: Round [190] log likelihood: -4021.204446
EM: Round [191] log likelihood: -4021.203846
EM: Round [192] log likelihood: -4021.203259
EM: Round [193] log likelihood: -4021.202686
EM: Round [194] log likelihood: -4021.202125
EM: Round [195] log likelihood: -4021.201577
EM: Round [196] log likelihood: -4021.201042
EM: Round [197] log likelihood: -4021.200518
EM: Round [198] log likelihood: -4021.200006
EM: Round [199] log likelihood: -4021.199506
EM: Round [200] log likelihood: -4021.199017
EM: Round [201] log likelihood: -4021.198538
EM: Round [202] log likelihood: -4021.198071
EM: Round [203] log likelihood: -4021.197614
EM: Round [204] log likelihood: -4021.197168
EM: Round [205] log likelihood: -4021.196731
EM: Round [206] log likelihood: -4021.196304
EM: Round [207] log likelihood: -4021.195887
EM: Round [208] log likelihood: -4021.195479
EM: Round [209] log likelihood: -4021.195080
EM: Round [210] log likelihood: -4021.194691
EM: Round [211] log likelihood: -4021.194310
EM: Round [212] log likelihood: -4021.193937
EM: Round [213] log likelihood: -4021.193573
EM: Round [214] log likelihood: -4021.193217
EM: Round [215] log likelihood: -4021.192869
EM: Round [216] log likelihood: -4021.192529
EM: Round [217] log likelihood: -4021.192197
EM: Round [218] log likelihood: -4021.191872
EM: Round [219] log likelihood: -4021.191554
EM: Round [220] log likelihood: -4021.191243
EM: Round [221] log likelihood: -4021.190940
EM: Round [222] log likelihood: -4021.190643
EM: Round [223] log likelihood: -4021.190352
EM: Round [224] log likelihood: -4021.190069
EM: Round [225] log likelihood: -4021.189791
EM: Round [226] log likelihood: -4021.189520
EM: Round [227] log likelihood: -4021.189255
EM: Round [228] log likelihood: -4021.188996
EM: Round [229] log likelihood: -4021.188743
EM: Round [230] log likelihood: -4021.188495
EM: Round [231] log likelihood: -4021.188253
EM: Round [232] log likelihood: -4021.188017
EM: Round [233] log likelihood: -4021.187785
EM: Round [234] log likelihood: -4021.187559
EM: Round [235] log likelihood: -4021.187338
EM: Round [236] log likelihood: -4021.187122
EM: Round [237] log likelihood: -4021.186911
EM: Round [238] log likelihood: -4021.186704
EM: Round [239] log likelihood: -4021.186502
EM: Round [240] log likelihood: -4021.186305
EM: Round [241] log likelihood: -4021.186112
EM: Round [242] log likelihood: -4021.185923
EM: Round [243] log likelihood: -4021.185739
EM: Round [244] log likelihood: -4021.185558
EM: Round [245] log likelihood: -4021.185382
EM: Round [246] log likelihood: -4021.185210
EM: Round [247] log likelihood: -4021.185041
EM: Round [248] log likelihood: -4021.184876
EM: Round [249] log likelihood: -4021.184715
EM: Round [250] log likelihood: -4021.184558
EM: Round [251] log likelihood: -4021.184404
EM: Round [252] log likelihood: -4021.184254
EM: Round [253] log likelihood: -4021.184107
EM: Round [254] log likelihood: -4021.183963
EM: Round [255] log likelihood: -4021.183822
EM: Round [256] log likelihood: -4021.183685
EM: Round [257] log likelihood: -4021.183550
EM: Round [258] log likelihood: -4021.183419
EM: Round [259] log likelihood: -4021.183291
EM: Round [260] log likelihood: -4021.183165
EM: Round [261] log likelihood: -4021.183043
EM: Round [262] log likelihood: -4021.182923
EM: Round [263] log likelihood: -4021.182805
EM: Round [264] log likelihood: -4021.182691
EM: Round [265] log likelihood: -4021.182579
EM: Round [266] log likelihood: -4021.182469
EM: Round [267] log likelihood: -4021.182362
EM: Round [268] log likelihood: -4021.182257
EM: Round [269] log likelihood: -4021.182155
EM: Round [270] log likelihood: -4021.182055
EM: Round [271] log likelihood: -4021.181957
EM: Stopping iterations at round 271 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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa > /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir
-done, see /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3892.496577
EM: Round [1] log likelihood: -3892.387347
EM: Round [2] log likelihood: -3892.386123
EM: Round [3] log likelihood: -3892.386096
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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296672127
Execution Time = 5.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yzUtTbjI1y/fi_workdir/microH.dat
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.yzUtTbjI1y/fi_workdir/microH.dat /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_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.yzUtTbjI1y/fi_workdir/microH.dat /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.yzUtTbjI1y --json_outfile /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.yzUtTbjI1y --json_outfile /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.yzUtTbjI1y/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.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1 --html_output /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-98fc22-R1_A23WJ53LT4_1 --html_output /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000255185.6]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.yzUtTbjI1y/ctat_genome_lib_build_dir > /tmp/nxf.yzUtTbjI1y/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.yzUtTbjI1y/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory