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/5b/a031f794fd70b39e21d0ce5843009c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/a031f794fd70b39e21d0ce5843009c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/b0204ddcef06a61fa7cebf56975c9e/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/a015d4c01e4dcfa3e47ff79f796064/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/a015d4c01e4dcfa3e47ff79f796064/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_2.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-87d1a3-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/cytoBand.txt
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.yYaO9l9d7J/fi_workdir --reads "/tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:23:04 ..... started STAR run
Jun 08 10:23:04 ..... loading genome
Jun 08 10:24:48 ... generating Suffix Array index
Jun 08 10:28:28 ... completed Suffix Array index
Jun 08 10:28:28 ..... processing annotations GTF
Jun 08 10:28:29 ..... inserting junctions into the genome indices
Jun 08 10:29:30 ..... started mapping
Jun 08 11:20:04 ..... finished mapping
Jun 08 11:20:05 ..... started sorting BAM
Jun 08 11:20:09 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 57.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.yYaO9l9d7J/fi_workdir --reads "/tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:21:04 : INFO : Done.
Execution Time = 0.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[9220000] -done parsing /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 36538,
'seq-similar region overlap' => 154,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 36,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 33,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1749,
'small anchor length' => 231,
'excessive soft clipping' => 68078,
'low complexity anchor region' => 51,
'num genes matched < 2' => 620,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 274,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 316,
'exons hit < 2' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 32,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1141,
' ** passed ** ' => 34327,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2
};
-writing fusion junction support info.
Execution Time = 5.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[78000] -fusion SPANNING read extraction for scaff: ARFGEF2--RNU7-173P
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[19000] -fusion SPANNING read extraction for scaff: BCCIP--FANK1
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[18000] -fusion SPANNING read extraction for scaff: BMS1P2--PTPN20
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[30000] -fusion SPANNING read extraction for scaff: BNIP1--CREBRF
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[83000] -fusion SPANNING read extraction for scaff: BORCS8--ADAMTS10
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[72000] -fusion SPANNING read extraction for scaff: C19orf48--KLK13
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[225000] -fusion SPANNING read extraction for scaff: CAPRIN1--DEPDC7
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[48000] -fusion SPANNING read extraction for scaff: CCDC7--POFUT1
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[214000] -fusion SPANNING read extraction for scaff: CD59--GJA5
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[101000] -fusion SPANNING read extraction for scaff: CELF1--KBTBD4
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[30000] -fusion SPANNING read extraction for scaff: CEP43--PDE10A
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[41000] -fusion SPANNING read extraction for scaff: CNOT2--AKAP3
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[54000] -fusion SPANNING read extraction for scaff: CSTF3--CCDC73
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[66000] -fusion SPANNING read extraction for scaff: CUX1--ELMO1
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[32000] -fusion SPANNING read extraction for scaff: CXADR--RSPH1
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[84000] -fusion SPANNING read extraction for scaff: CXADR--RRP1B
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[437000] -fusion SPANNING read extraction for scaff: DNM3--NFIB
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[221000] -fusion SPANNING read extraction for scaff: EHF--CAT
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[264000] -fusion SPANNING read extraction for scaff: EIF4A2--RFC4
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[62000] -fusion SPANNING read extraction for scaff: EXD3--PNPLA7
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[44000] -fusion SPANNING read extraction for scaff: GALNT16--RAD51B
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[142000] -fusion SPANNING read extraction for scaff: GNB1--NADK
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[33000] -fusion SPANNING read extraction for scaff: GRB10--AC079801.1
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[33000] -fusion SPANNING read extraction for scaff: GRB10--LINC01670
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[19000] -fusion SPANNING read extraction for scaff: GTF2H2C--AC010267.1
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[19000] -fusion SPANNING read extraction for scaff: GTF2H2C--AC093534.1
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[87000] -fusion SPANNING read extraction for scaff: KIAA0232--WFS1
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[22000] -fusion SPANNING read extraction for scaff: KLF11--ZNF804A
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[21000] -fusion SPANNING read extraction for scaff: KLF11--AC009315.1
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[129000] -fusion SPANNING read extraction for scaff: LDHA--AP001102.1
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[154000] -fusion SPANNING read extraction for scaff: LDHA--TMEM135
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[27000] -fusion SPANNING read extraction for scaff: LHFPL5--CLPSL1
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[68000] -fusion SPANNING read extraction for scaff: LRRC24--TYMS
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[31000] -fusion SPANNING read extraction for scaff: MARK4--CDRT15P9
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[41000] -fusion SPANNING read extraction for scaff: MPND--AC104521.1
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[48000] -fusion SPANNING read extraction for scaff: MRPL14--COL21A1
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[149000] -fusion SPANNING read extraction for scaff: MSN--NAV2
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[155000] -fusion SPANNING read extraction for scaff: MVB12B--SERP1
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[48000] -fusion SPANNING read extraction for scaff: NARS2--GAB2
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[96000] -fusion SPANNING read extraction for scaff: NF1--ZMIZ1
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[1090000] -fusion SPANNING read extraction for scaff: NOTCH2NLC--SND1
[1000]
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
[1000]
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
[1000]
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
[1000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
[1000]
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[39000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[39000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[63000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[30000] -fusion SPANNING read extraction for scaff: PDE10A--CEP43
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[82000] -fusion SPANNING read extraction for scaff: PEBP1--FBXW8
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[110000] -fusion SPANNING read extraction for scaff: PIGS--SPAG5
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[31000] -fusion SPANNING read extraction for scaff: PIP4K2B--LHX1-DT
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[3000] -fusion SPANNING read extraction for scaff: PRRG1--AL592156.1
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[3000] -fusion SPANNING read extraction for scaff: PRRG1--BX842568.3
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[292000] -fusion SPANNING read extraction for scaff: QKI--PACRG
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[60000] -fusion SPANNING read extraction for scaff: RAB6A--MPP7
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[120000] -fusion SPANNING read extraction for scaff: RMND5A--ANAPC1
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[12000] -fusion SPANNING read extraction for scaff: RNF150--AL359232.1
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[57000] -fusion SPANNING read extraction for scaff: RRP1B--RSPH1
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[81000] -fusion SPANNING read extraction for scaff: SH3BP2--FAM53A
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[55000] -fusion SPANNING read extraction for scaff: TBC1D31--FRMD4A
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[41000] -fusion SPANNING read extraction for scaff: TBC1D9--RNF150
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[24000] -fusion SPANNING read extraction for scaff: TBCK--RNU6-173P
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[24000] -fusion SPANNING read extraction for scaff: TBCK--TRIML1
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[64000] -fusion SPANNING read extraction for scaff: TEX261--MYO1F
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[47000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[26000] -fusion SPANNING read extraction for scaff: TMTC2--AC089998.1
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[27000] -fusion SPANNING read extraction for scaff: TMTC2--AC091214.1
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[188000] -fusion SPANNING read extraction for scaff: TRAPPC9--SLC45A4
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[58000] -fusion SPANNING read extraction for scaff: TXN2--FOXRED2
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[104000] -fusion SPANNING read extraction for scaff: UHRF1--AC024610.2
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[104000] -fusion SPANNING read extraction for scaff: UHRF1--ASIC2
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[76000] -fusion SPANNING read extraction for scaff: VMP1--RPS6KB1
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[242000] -fusion SPANNING read extraction for scaff: VPS13B--AGK
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[25000] -fusion SPANNING read extraction for scaff: VTA1--HSF2
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[299000] -fusion SPANNING read extraction for scaff: WWTR1--C21orf91-OT1
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[95000] -fusion SPANNING read extraction for scaff: YWHAQ--IHO1
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[8000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
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[8000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
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[42000] -fusion SPANNING read extraction for scaff: ZNF626--FARP2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 48174,
'lacks exon overlap' => 111645
};
Execution Time = 14.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -54345.953837
EM: Round [1] log likelihood: -54340.124695
EM: Round [2] log likelihood: -54340.112190
EM: Round [3] log likelihood: -54340.102020
EM: Round [4] log likelihood: -54340.091792
EM: Round [5] log likelihood: -54340.081501
EM: Round [6] log likelihood: -54340.071147
EM: Round [7] log likelihood: -54340.060734
EM: Round [8] log likelihood: -54340.050262
EM: Round [9] log likelihood: -54340.039735
EM: Round [10] log likelihood: -54340.029153
EM: Round [11] log likelihood: -54340.018520
EM: Round [12] log likelihood: -54340.007837
EM: Round [13] log likelihood: -54339.997107
EM: Round [14] log likelihood: -54339.986331
EM: Round [15] log likelihood: -54339.975512
EM: Round [16] log likelihood: -54339.964651
EM: Round [17] log likelihood: -54339.953752
EM: Round [18] log likelihood: -54339.942816
EM: Round [19] log likelihood: -54339.931846
EM: Round [20] log likelihood: -54339.920843
EM: Round [21] log likelihood: -54339.909810
EM: Round [22] log likelihood: -54339.898749
EM: Round [23] log likelihood: -54339.887662
EM: Round [24] log likelihood: -54339.876553
EM: Round [25] log likelihood: -54339.865421
EM: Round [26] log likelihood: -54339.854271
EM: Round [27] log likelihood: -54339.843104
EM: Round [28] log likelihood: -54339.831923
EM: Round [29] log likelihood: -54339.820729
EM: Round [30] log likelihood: -54339.809525
EM: Round [31] log likelihood: -54339.798312
EM: Round [32] log likelihood: -54339.787094
EM: Round [33] log likelihood: -54339.775872
EM: Round [34] log likelihood: -54339.764648
EM: Round [35] log likelihood: -54339.753425
EM: Round [36] log likelihood: -54339.742204
EM: Round [37] log likelihood: -54339.730987
EM: Round [38] log likelihood: -54339.719776
EM: Round [39] log likelihood: -54339.708575
EM: Round [40] log likelihood: -54339.697383
EM: Round [41] log likelihood: -54339.686204
EM: Round [42] log likelihood: -54339.675039
EM: Round [43] log likelihood: -54339.663889
EM: Round [44] log likelihood: -54339.652758
EM: Round [45] log likelihood: -54339.641647
EM: Round [46] log likelihood: -54339.630556
EM: Round [47] log likelihood: -54339.619489
EM: Round [48] log likelihood: -54339.608447
EM: Round [49] log likelihood: -54339.597431
EM: Round [50] log likelihood: -54339.586444
EM: Round [51] log likelihood: -54339.575486
EM: Round [52] log likelihood: -54339.564559
EM: Round [53] log likelihood: -54339.553665
EM: Round [54] log likelihood: -54339.542805
EM: Round [55] log likelihood: -54339.531981
EM: Round [56] log likelihood: -54339.521193
EM: Round [57] log likelihood: -54339.510444
EM: Round [58] log likelihood: -54339.499735
EM: Round [59] log likelihood: -54339.489067
EM: Round [60] log likelihood: -54339.478441
EM: Round [61] log likelihood: -54339.467858
EM: Round [62] log likelihood: -54339.457320
EM: Round [63] log likelihood: -54339.446827
EM: Round [64] log likelihood: -54339.436381
EM: Round [65] log likelihood: -54339.425983
EM: Round [66] log likelihood: -54339.415634
EM: Round [67] log likelihood: -54339.405334
EM: Round [68] log likelihood: -54339.395085
EM: Round [69] log likelihood: -54339.384888
EM: Round [70] log likelihood: -54339.374742
EM: Round [71] log likelihood: -54339.364650
EM: Round [72] log likelihood: -54339.354612
EM: Round [73] log likelihood: -54339.344629
EM: Round [74] log likelihood: -54339.334701
EM: Round [75] log likelihood: -54339.324829
EM: Round [76] log likelihood: -54339.315014
EM: Round [77] log likelihood: -54339.305256
EM: Round [78] log likelihood: -54339.295556
EM: Round [79] log likelihood: -54339.285915
EM: Round [80] log likelihood: -54339.276332
EM: Round [81] log likelihood: -54339.266808
EM: Round [82] log likelihood: -54339.257345
EM: Round [83] log likelihood: -54339.247942
EM: Round [84] log likelihood: -54339.238599
EM: Round [85] log likelihood: -54339.229317
EM: Round [86] log likelihood: -54339.220096
EM: Round [87] log likelihood: -54339.210937
EM: Round [88] log likelihood: -54339.201840
EM: Round [89] log likelihood: -54339.192805
EM: Round [90] log likelihood: -54339.183832
EM: Round [91] log likelihood: -54339.174921
EM: Round [92] log likelihood: -54339.166073
EM: Round [93] log likelihood: -54339.157288
EM: Round [94] log likelihood: -54339.148566
EM: Round [95] log likelihood: -54339.139906
EM: Round [96] log likelihood: -54339.131310
EM: Round [97] log likelihood: -54339.122776
EM: Round [98] log likelihood: -54339.114306
EM: Round [99] log likelihood: -54339.105899
EM: Round [100] log likelihood: -54339.097554
EM: Round [101] log likelihood: -54339.089273
EM: Round [102] log likelihood: -54339.081055
EM: Round [103] log likelihood: -54339.072899
EM: Round [104] log likelihood: -54339.064806
EM: Round [105] log likelihood: -54339.056776
EM: Round [106] log likelihood: -54339.048809
EM: Round [107] log likelihood: -54339.040904
EM: Round [108] log likelihood: -54339.033061
EM: Round [109] log likelihood: -54339.025280
EM: Round [110] log likelihood: -54339.017561
EM: Round [111] log likelihood: -54339.009904
EM: Round [112] log likelihood: -54339.002308
EM: Round [113] log likelihood: -54338.994774
EM: Round [114] log likelihood: -54338.987300
EM: Round [115] log likelihood: -54338.979888
EM: Round [116] log likelihood: -54338.972536
EM: Round [117] log likelihood: -54338.965244
EM: Round [118] log likelihood: -54338.958012
EM: Round [119] log likelihood: -54338.950839
EM: Round [120] log likelihood: -54338.943727
EM: Round [121] log likelihood: -54338.936673
EM: Round [122] log likelihood: -54338.929678
EM: Round [123] log likelihood: -54338.922741
EM: Round [124] log likelihood: -54338.915862
EM: Round [125] log likelihood: -54338.909042
EM: Round [126] log likelihood: -54338.902278
EM: Round [127] log likelihood: -54338.895572
EM: Round [128] log likelihood: -54338.888922
EM: Round [129] log likelihood: -54338.882329
EM: Round [130] log likelihood: -54338.875792
EM: Round [131] log likelihood: -54338.869310
EM: Round [132] log likelihood: -54338.862884
EM: Round [133] log likelihood: -54338.856512
EM: Round [134] log likelihood: -54338.850195
EM: Round [135] log likelihood: -54338.843932
EM: Round [136] log likelihood: -54338.837722
EM: Round [137] log likelihood: -54338.831566
EM: Round [138] log likelihood: -54338.825462
EM: Round [139] log likelihood: -54338.819412
EM: Round [140] log likelihood: -54338.813413
EM: Round [141] log likelihood: -54338.807466
EM: Round [142] log likelihood: -54338.801570
EM: Round [143] log likelihood: -54338.795725
EM: Round [144] log likelihood: -54338.789930
EM: Round [145] log likelihood: -54338.784185
EM: Round [146] log likelihood: -54338.778490
EM: Round [147] log likelihood: -54338.772844
EM: Round [148] log likelihood: -54338.767247
EM: Round [149] log likelihood: -54338.761698
EM: Round [150] log likelihood: -54338.756197
EM: Round [151] log likelihood: -54338.750744
EM: Round [152] log likelihood: -54338.745338
EM: Round [153] log likelihood: -54338.739978
EM: Round [154] log likelihood: -54338.734665
EM: Round [155] log likelihood: -54338.729397
EM: Round [156] log likelihood: -54338.724175
EM: Round [157] log likelihood: -54338.718998
EM: Round [158] log likelihood: -54338.713865
EM: Round [159] log likelihood: -54338.708777
EM: Round [160] log likelihood: -54338.703733
EM: Round [161] log likelihood: -54338.698732
EM: Round [162] log likelihood: -54338.693773
EM: Round [163] log likelihood: -54338.688858
EM: Round [164] log likelihood: -54338.683984
EM: Round [165] log likelihood: -54338.679153
EM: Round [166] log likelihood: -54338.674362
EM: Round [167] log likelihood: -54338.669613
EM: Round [168] log likelihood: -54338.664904
EM: Round [169] log likelihood: -54338.660235
EM: Round [170] log likelihood: -54338.655607
EM: Round [171] log likelihood: -54338.651017
EM: Round [172] log likelihood: -54338.646467
EM: Round [173] log likelihood: -54338.641955
EM: Round [174] log likelihood: -54338.637481
EM: Round [175] log likelihood: -54338.633045
EM: Round [176] log likelihood: -54338.628647
EM: Round [177] log likelihood: -54338.624285
EM: Round [178] log likelihood: -54338.619961
EM: Round [179] log likelihood: -54338.615672
EM: Round [180] log likelihood: -54338.611420
EM: Round [181] log likelihood: -54338.607203
EM: Round [182] log likelihood: -54338.603022
EM: Round [183] log likelihood: -54338.598875
EM: Round [184] log likelihood: -54338.594763
EM: Round [185] log likelihood: -54338.590685
EM: Round [186] log likelihood: -54338.586641
EM: Round [187] log likelihood: -54338.582631
EM: Round [188] log likelihood: -54338.578653
EM: Round [189] log likelihood: -54338.574709
EM: Round [190] log likelihood: -54338.570797
EM: Round [191] log likelihood: -54338.566917
EM: Round [192] log likelihood: -54338.563068
EM: Round [193] log likelihood: -54338.559251
EM: Round [194] log likelihood: -54338.555466
EM: Round [195] log likelihood: -54338.551711
EM: Round [196] log likelihood: -54338.547986
EM: Round [197] log likelihood: -54338.544292
EM: Round [198] log likelihood: -54338.540628
EM: Round [199] log likelihood: -54338.536993
EM: Round [200] log likelihood: -54338.533387
EM: Round [201] log likelihood: -54338.529811
EM: Round [202] log likelihood: -54338.526263
EM: Round [203] log likelihood: -54338.522743
EM: Round [204] log likelihood: -54338.519251
EM: Round [205] log likelihood: -54338.515787
EM: Round [206] log likelihood: -54338.512351
EM: Round [207] log likelihood: -54338.508941
EM: Round [208] log likelihood: -54338.505559
EM: Round [209] log likelihood: -54338.502203
EM: Round [210] log likelihood: -54338.498873
EM: Round [211] log likelihood: -54338.495570
EM: Round [212] log likelihood: -54338.492292
EM: Round [213] log likelihood: -54338.489040
EM: Round [214] log likelihood: -54338.485812
EM: Round [215] log likelihood: -54338.482610
EM: Round [216] log likelihood: -54338.479433
EM: Round [217] log likelihood: -54338.476280
EM: Round [218] log likelihood: -54338.473151
EM: Round [219] log likelihood: -54338.470046
EM: Round [220] log likelihood: -54338.466965
EM: Round [221] log likelihood: -54338.463907
EM: Round [222] log likelihood: -54338.460873
EM: Round [223] log likelihood: -54338.457861
EM: Round [224] log likelihood: -54338.454872
EM: Round [225] log likelihood: -54338.451906
EM: Round [226] log likelihood: -54338.448962
EM: Round [227] log likelihood: -54338.446040
EM: Round [228] log likelihood: -54338.443139
EM: Round [229] log likelihood: -54338.440260
EM: Round [230] log likelihood: -54338.437403
EM: Round [231] log likelihood: -54338.434567
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EM: Round [693] log likelihood: -54337.975431
EM: Round [694] log likelihood: -54337.975143
EM: Round [695] log likelihood: -54337.974857
EM: Round [696] log likelihood: -54337.974571
EM: Round [697] log likelihood: -54337.974287
EM: Round [698] log likelihood: -54337.974004
EM: Round [699] log likelihood: -54337.973722
EM: Round [700] log likelihood: -54337.973441
EM: Round [701] log likelihood: -54337.973161
EM: Round [702] log likelihood: -54337.972883
EM: Round [703] log likelihood: -54337.972605
EM: Round [704] log likelihood: -54337.972329
EM: Round [705] log likelihood: -54337.972054
EM: Round [706] log likelihood: -54337.971780
EM: Round [707] log likelihood: -54337.971507
EM: Round [708] log likelihood: -54337.971235
EM: Round [709] log likelihood: -54337.970964
EM: Round [710] log likelihood: -54337.970694
EM: Round [711] log likelihood: -54337.970425
EM: Round [712] log likelihood: -54337.970158
EM: Round [713] log likelihood: -54337.969891
EM: Round [714] log likelihood: -54337.969626
EM: Round [715] log likelihood: -54337.969362
EM: Round [716] log likelihood: -54337.969098
EM: Round [717] log likelihood: -54337.968836
EM: Round [718] log likelihood: -54337.968575
EM: Round [719] log likelihood: -54337.968315
EM: Round [720] log likelihood: -54337.968056
EM: Round [721] log likelihood: -54337.967798
EM: Round [722] log likelihood: -54337.967541
EM: Round [723] log likelihood: -54337.967285
EM: Round [724] log likelihood: -54337.967030
EM: Round [725] log likelihood: -54337.966776
EM: Round [726] log likelihood: -54337.966523
EM: Round [727] log likelihood: -54337.966271
EM: Round [728] log likelihood: -54337.966020
EM: Round [729] log likelihood: -54337.965770
EM: Round [730] log likelihood: -54337.965521
EM: Round [731] log likelihood: -54337.965274
EM: Round [732] log likelihood: -54337.965027
EM: Round [733] log likelihood: -54337.964781
EM: Round [734] log likelihood: -54337.964536
EM: Round [735] log likelihood: -54337.964292
EM: Round [736] log likelihood: -54337.964049
EM: Round [737] log likelihood: -54337.963807
EM: Round [738] log likelihood: -54337.963566
EM: Round [739] log likelihood: -54337.963326
EM: Round [740] log likelihood: -54337.963087
EM: Round [741] log likelihood: -54337.962849
EM: Round [742] log likelihood: -54337.962612
EM: Round [743] log likelihood: -54337.962375
EM: Round [744] log likelihood: -54337.962140
EM: Round [745] log likelihood: -54337.961906
EM: Round [746] log likelihood: -54337.961672
EM: Round [747] log likelihood: -54337.961440
EM: Round [748] log likelihood: -54337.961208
EM: Round [749] log likelihood: -54337.960978
EM: Round [750] log likelihood: -54337.960748
EM: Round [751] log likelihood: -54337.960519
EM: Round [752] log likelihood: -54337.960291
EM: Round [753] log likelihood: -54337.960064
EM: Round [754] log likelihood: -54337.959838
EM: Round [755] log likelihood: -54337.959613
EM: Round [756] log likelihood: -54337.959389
EM: Round [757] log likelihood: -54337.959165
EM: Round [758] log likelihood: -54337.958943
EM: Round [759] log likelihood: -54337.958721
EM: Round [760] log likelihood: -54337.958500
EM: Round [761] log likelihood: -54337.958281
EM: Round [762] log likelihood: -54337.958062
EM: Round [763] log likelihood: -54337.957843
EM: Round [764] log likelihood: -54337.957626
EM: Round [765] log likelihood: -54337.957410
EM: Round [766] log likelihood: -54337.957194
EM: Round [767] log likelihood: -54337.956980
EM: Round [768] log likelihood: -54337.956766
EM: Round [769] log likelihood: -54337.956553
EM: Round [770] log likelihood: -54337.956341
EM: Round [771] log likelihood: -54337.956130
EM: Round [772] log likelihood: -54337.955919
EM: Round [773] log likelihood: -54337.955710
EM: Round [774] log likelihood: -54337.955501
EM: Round [775] log likelihood: -54337.955293
EM: Round [776] log likelihood: -54337.955086
EM: Round [777] log likelihood: -54337.954879
EM: Round [778] log likelihood: -54337.954674
EM: Round [779] log likelihood: -54337.954469
EM: Round [780] log likelihood: -54337.954265
EM: Round [781] log likelihood: -54337.954062
EM: Round [782] log likelihood: -54337.953860
EM: Round [783] log likelihood: -54337.953659
EM: Round [784] log likelihood: -54337.953458
EM: Round [785] log likelihood: -54337.953258
EM: Round [786] log likelihood: -54337.953059
EM: Round [787] log likelihood: -54337.952861
EM: Round [788] log likelihood: -54337.952663
EM: Round [789] log likelihood: -54337.952467
EM: Round [790] log likelihood: -54337.952271
EM: Round [791] log likelihood: -54337.952076
EM: Round [792] log likelihood: -54337.951881
EM: Round [793] log likelihood: -54337.951688
EM: Round [794] log likelihood: -54337.951495
EM: Round [795] log likelihood: -54337.951303
EM: Round [796] log likelihood: -54337.951111
EM: Round [797] log likelihood: -54337.950921
EM: Round [798] log likelihood: -54337.950731
EM: Round [799] log likelihood: -54337.950542
EM: Round [800] log likelihood: -54337.950354
EM: Round [801] log likelihood: -54337.950166
EM: Round [802] log likelihood: -54337.949979
EM: Round [803] log likelihood: -54337.949793
EM: Round [804] log likelihood: -54337.949608
EM: Round [805] log likelihood: -54337.949423
EM: Round [806] log likelihood: -54337.949239
EM: Round [807] log likelihood: -54337.949056
EM: Round [808] log likelihood: -54337.948874
EM: Round [809] log likelihood: -54337.948692
EM: Round [810] log likelihood: -54337.948511
EM: Round [811] log likelihood: -54337.948330
EM: Round [812] log likelihood: -54337.948151
EM: Round [813] log likelihood: -54337.947972
EM: Round [814] log likelihood: -54337.947794
EM: Round [815] log likelihood: -54337.947616
EM: Round [816] log likelihood: -54337.947440
EM: Round [817] log likelihood: -54337.947263
EM: Round [818] log likelihood: -54337.947088
EM: Round [819] log likelihood: -54337.946913
EM: Round [820] log likelihood: -54337.946739
EM: Round [821] log likelihood: -54337.946566
EM: Round [822] log likelihood: -54337.946393
EM: Round [823] log likelihood: -54337.946221
EM: Round [824] log likelihood: -54337.946050
EM: Round [825] log likelihood: -54337.945879
EM: Round [826] log likelihood: -54337.945709
EM: Round [827] log likelihood: -54337.945540
EM: Round [828] log likelihood: -54337.945371
EM: Round [829] log likelihood: -54337.945203
EM: Round [830] log likelihood: -54337.945036
EM: Round [831] log likelihood: -54337.944870
EM: Round [832] log likelihood: -54337.944704
EM: Round [833] log likelihood: -54337.944538
EM: Round [834] log likelihood: -54337.944373
EM: Round [835] log likelihood: -54337.944209
EM: Round [836] log likelihood: -54337.944046
EM: Round [837] log likelihood: -54337.943883
EM: Round [838] log likelihood: -54337.943721
EM: Round [839] log likelihood: -54337.943560
EM: Round [840] log likelihood: -54337.943399
EM: Round [841] log likelihood: -54337.943239
EM: Round [842] log likelihood: -54337.943079
EM: Round [843] log likelihood: -54337.942920
EM: Round [844] log likelihood: -54337.942762
EM: Round [845] log likelihood: -54337.942604
EM: Round [846] log likelihood: -54337.942447
EM: Round [847] log likelihood: -54337.942290
EM: Round [848] log likelihood: -54337.942134
EM: Round [849] log likelihood: -54337.941979
EM: Round [850] log likelihood: -54337.941824
EM: Round [851] log likelihood: -54337.941670
EM: Round [852] log likelihood: -54337.941517
EM: Round [853] log likelihood: -54337.941364
EM: Round [854] log likelihood: -54337.941212
EM: Round [855] log likelihood: -54337.941060
EM: Round [856] log likelihood: -54337.940909
EM: Round [857] log likelihood: -54337.940758
EM: Round [858] log likelihood: -54337.940609
EM: Round [859] log likelihood: -54337.940459
EM: Round [860] log likelihood: -54337.940311
EM: Round [861] log likelihood: -54337.940162
EM: Round [862] log likelihood: -54337.940015
EM: Round [863] log likelihood: -54337.939868
EM: Round [864] log likelihood: -54337.939721
EM: Round [865] log likelihood: -54337.939576
EM: Round [866] log likelihood: -54337.939430
EM: Round [867] log likelihood: -54337.939286
EM: Round [868] log likelihood: -54337.939141
EM: Round [869] log likelihood: -54337.938998
EM: Round [870] log likelihood: -54337.938855
EM: Round [871] log likelihood: -54337.938712
EM: Round [872] log likelihood: -54337.938570
EM: Round [873] log likelihood: -54337.938429
EM: Round [874] log likelihood: -54337.938288
EM: Round [875] log likelihood: -54337.938148
EM: Round [876] log likelihood: -54337.938008
EM: Round [877] log likelihood: -54337.937869
EM: Round [878] log likelihood: -54337.937730
EM: Round [879] log likelihood: -54337.937592
EM: Round [880] log likelihood: -54337.937455
EM: Round [881] log likelihood: -54337.937318
EM: Round [882] log likelihood: -54337.937181
EM: Round [883] log likelihood: -54337.937045
EM: Round [884] log likelihood: -54337.936910
EM: Round [885] log likelihood: -54337.936775
EM: Round [886] log likelihood: -54337.936641
EM: Round [887] log likelihood: -54337.936507
EM: Round [888] log likelihood: -54337.936374
EM: Round [889] log likelihood: -54337.936241
EM: Round [890] log likelihood: -54337.936108
EM: Round [891] log likelihood: -54337.935977
EM: Round [892] log likelihood: -54337.935845
EM: Round [893] log likelihood: -54337.935715
EM: Round [894] log likelihood: -54337.935584
EM: Round [895] log likelihood: -54337.935455
EM: Round [896] log likelihood: -54337.935325
EM: Round [897] log likelihood: -54337.935197
EM: Round [898] log likelihood: -54337.935069
EM: Round [899] log likelihood: -54337.934941
EM: Round [900] log likelihood: -54337.934814
EM: Round [901] log likelihood: -54337.934687
EM: Round [902] log likelihood: -54337.934561
EM: Round [903] log likelihood: -54337.934435
EM: Round [904] log likelihood: -54337.934310
EM: Round [905] log likelihood: -54337.934185
EM: Round [906] log likelihood: -54337.934061
EM: Round [907] log likelihood: -54337.933937
EM: Round [908] log likelihood: -54337.933813
EM: Round [909] log likelihood: -54337.933691
EM: Round [910] log likelihood: -54337.933568
EM: Round [911] log likelihood: -54337.933446
EM: Round [912] log likelihood: -54337.933325
EM: Round [913] log likelihood: -54337.933204
EM: Round [914] log likelihood: -54337.933083
EM: Round [915] log likelihood: -54337.932963
EM: Round [916] log likelihood: -54337.932844
EM: Round [917] log likelihood: -54337.932725
EM: Round [918] log likelihood: -54337.932606
EM: Round [919] log likelihood: -54337.932488
EM: Round [920] log likelihood: -54337.932370
EM: Round [921] log likelihood: -54337.932253
EM: Round [922] log likelihood: -54337.932136
EM: Round [923] log likelihood: -54337.932020
EM: Round [924] log likelihood: -54337.931904
EM: Round [925] log likelihood: -54337.931788
EM: Round [926] log likelihood: -54337.931673
EM: Round [927] log likelihood: -54337.931559
EM: Round [928] log likelihood: -54337.931445
EM: Round [929] log likelihood: -54337.931331
EM: Round [930] log likelihood: -54337.931218
EM: Round [931] log likelihood: -54337.931105
EM: Round [932] log likelihood: -54337.930993
EM: Round [933] log likelihood: -54337.930881
EM: Round [934] log likelihood: -54337.930769
EM: Round [935] log likelihood: -54337.930658
EM: Round [936] log likelihood: -54337.930548
EM: Round [937] log likelihood: -54337.930437
EM: Round [938] log likelihood: -54337.930328
EM: Round [939] log likelihood: -54337.930218
EM: Round [940] log likelihood: -54337.930109
EM: Round [941] log likelihood: -54337.930001
EM: Round [942] log likelihood: -54337.929893
EM: Round [943] log likelihood: -54337.929785
EM: Round [944] log likelihood: -54337.929678
EM: Round [945] log likelihood: -54337.929571
EM: Round [946] log likelihood: -54337.929465
EM: Round [947] log likelihood: -54337.929359
EM: Round [948] log likelihood: -54337.929253
EM: Round [949] log likelihood: -54337.929148
EM: Round [950] log likelihood: -54337.929043
EM: Round [951] log likelihood: -54337.928939
EM: Round [952] log likelihood: -54337.928835
EM: Round [953] log likelihood: -54337.928731
EM: Round [954] log likelihood: -54337.928628
EM: Round [955] log likelihood: -54337.928525
EM: Round [956] log likelihood: -54337.928423
EM: Round [957] log likelihood: -54337.928321
EM: Round [958] log likelihood: -54337.928219
EM: Round [959] log likelihood: -54337.928118
EM: Round [960] log likelihood: -54337.928017
EM: Round [961] log likelihood: -54337.927917
EM: Round [962] log likelihood: -54337.927817
EM: Round [963] log likelihood: -54337.927717
EM: Stopping iterations at round 963 due to insufficient improvement in likelihood.
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 2.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa > /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir
-done, see /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -50307.390591
EM: Round [1] log likelihood: -50305.808869
EM: Round [2] log likelihood: -50305.807926
EM: Round [3] log likelihood: -50305.807923
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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296795392
Execution Time = 5.63 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gtf > /tmp/nxf.yYaO9l9d7J/fi_workdir/microH.dat
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.yYaO9l9d7J/fi_workdir/microH.dat /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/fi_workdir/microH.dat /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.yYaO9l9d7J --json_outfile /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-87d1a3-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.yYaO9l9d7J --json_outfile /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.yYaO9l9d7J/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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1 --html_output /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.04 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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1 --html_output /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-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.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000167747.15]
WARNING, no entry stored in dbm for [ENSG00000167747.15]
WARNING, no entry stored in dbm for [ENSG00000167747.15]
WARNING, no entry stored in dbm for [ENSG00000279668.3]
WARNING, no entry stored in dbm for [ENSG00000279668.3]
WARNING, no entry stored in dbm for [ENSG00000279668.3]
WARNING, no entry stored in dbm for [ENSG00000277268.2]
WARNING, no entry stored in dbm for [ENSG00000277268.2]
WARNING, no entry stored in dbm for [ENSG00000277268.2]
WARNING, no entry stored in dbm for [ENSG00000277268.2]
WARNING, no entry stored in dbm for [ENSG00000277268.2]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
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 [ENSG00000253438.4]
WARNING, no entry stored in dbm for [ENSG00000253438.4]
WARNING, no entry stored in dbm for [ENSG00000240770.5]
WARNING, no entry stored in dbm for [ENSG00000240770.5]
WARNING, no entry stored in dbm for [ENSG00000269425.1]
WARNING, no entry stored in dbm for [ENSG00000269425.1]
WARNING, no entry stored in dbm for [ENSG00000238122.1]
WARNING, no entry stored in dbm for [ENSG00000285373.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000279414.1]
WARNING, no entry stored in dbm for [ENSG00000213287.3]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.yYaO9l9d7J/ctat_genome_lib_build_dir > /tmp/nxf.yYaO9l9d7J/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.yYaO9l9d7J/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory