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/c1/edf009011700c31e2f2edf2008342d/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/9412579eca0feef07c4535c1bb6d97/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/edf009011700c31e2f2edf2008342d/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/9412579eca0feef07c4535c1bb6d97/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/f84db8aaa855293d5b750c74159491/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_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-5519ab-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/cytoBand.txt
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.bbugZeEaKv/fi_workdir --reads "/tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 03 21:05:19 ..... started STAR run
Jun 03 21:05:19 ..... loading genome
Jun 03 21:07:03 ... generating Suffix Array index
Jun 03 21:10:57 ... completed Suffix Array index
Jun 03 21:10:57 ..... processing annotations GTF
Jun 03 21:10:58 ..... inserting junctions into the genome indices
Jun 03 21:11:59 ..... started mapping
Jun 03 22:20:28 ..... finished mapping
Jun 03 22:20:30 ..... started sorting BAM
Jun 03 22:20:31 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 75.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.bbugZeEaKv/fi_workdir --reads "/tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
22:20:44 : INFO : Done.
Execution Time = 0.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[2260000] -done parsing /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 15696,
'small anchor length' => 99,
'low complexity anchor region' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10,
'per_id < 96' => 6545,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 45,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 24,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 23,
'seq-similar region overlap' => 772,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 63,
'excessive soft clipping' => 9581,
'num genes matched < 2' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 84
};
-writing fusion junction support info.
Execution Time = 1.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[64000] -fusion SPANNING read extraction for scaff: NRG4--TBCA
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[46000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[49000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[38000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[151000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[80000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[88000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[110000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[97000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[54000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[36000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[151000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[88000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[97000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[54000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[102000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[79000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
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[5000] -fusion SPANNING read extraction for scaff: RNU6-138P--KCNH8
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[48000] -fusion SPANNING read extraction for scaff: SBF2--PPIAP86
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[48000] -fusion SPANNING read extraction for scaff: SBF2--LINC01299
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[47000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[109000] -fusion SPANNING read extraction for scaff: UBE2O--ZIC1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 320602,
'lacks exon overlap' => 5199
};
Execution Time = 2.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6778.137456
EM: Round [1] log likelihood: -6739.644749
EM: Round [2] log likelihood: -6728.827591
EM: Round [3] log likelihood: -6725.615996
EM: Round [4] log likelihood: -6724.452836
EM: Round [5] log likelihood: -6723.818725
EM: Round [6] log likelihood: -6723.337296
EM: Round [7] log likelihood: -6722.921730
EM: Round [8] log likelihood: -6722.550258
EM: Round [9] log likelihood: -6722.214967
EM: Round [10] log likelihood: -6721.911178
EM: Round [11] log likelihood: -6721.635280
EM: Round [12] log likelihood: -6721.384234
EM: Round [13] log likelihood: -6721.155419
EM: Round [14] log likelihood: -6720.946546
EM: Round [15] log likelihood: -6720.755606
EM: Round [16] log likelihood: -6720.580829
EM: Round [17] log likelihood: -6720.420645
EM: Round [18] log likelihood: -6720.273658
EM: Round [19] log likelihood: -6720.138627
EM: Round [20] log likelihood: -6720.014440
EM: Round [21] log likelihood: -6719.900101
EM: Round [22] log likelihood: -6719.794717
EM: Round [23] log likelihood: -6719.697486
EM: Round [24] log likelihood: -6719.607684
EM: Round [25] log likelihood: -6719.524658
EM: Round [26] log likelihood: -6719.447820
EM: Round [27] log likelihood: -6719.376637
EM: Round [28] log likelihood: -6719.310628
EM: Round [29] log likelihood: -6719.249355
EM: Round [30] log likelihood: -6719.192424
EM: Round [31] log likelihood: -6719.139473
EM: Round [32] log likelihood: -6719.090177
EM: Round [33] log likelihood: -6719.044240
EM: Round [34] log likelihood: -6719.001389
EM: Round [35] log likelihood: -6718.961381
EM: Round [36] log likelihood: -6718.923990
EM: Round [37] log likelihood: -6718.889012
EM: Round [38] log likelihood: -6718.856260
EM: Round [39] log likelihood: -6718.825564
EM: Round [40] log likelihood: -6718.796768
EM: Round [41] log likelihood: -6718.769730
EM: Round [42] log likelihood: -6718.744319
EM: Round [43] log likelihood: -6718.720416
EM: Round [44] log likelihood: -6718.697912
EM: Round [45] log likelihood: -6718.676705
EM: Round [46] log likelihood: -6718.656705
EM: Round [47] log likelihood: -6718.637825
EM: Round [48] log likelihood: -6718.619990
EM: Round [49] log likelihood: -6718.603127
EM: Round [50] log likelihood: -6718.587170
EM: Round [51] log likelihood: -6718.572059
EM: Round [52] log likelihood: -6718.557739
EM: Round [53] log likelihood: -6718.544157
EM: Round [54] log likelihood: -6718.531266
EM: Round [55] log likelihood: -6718.519022
EM: Round [56] log likelihood: -6718.507385
EM: Round [57] log likelihood: -6718.496317
EM: Round [58] log likelihood: -6718.485783
EM: Round [59] log likelihood: -6718.475752
EM: Round [60] log likelihood: -6718.466193
EM: Round [61] log likelihood: -6718.457079
EM: Round [62] log likelihood: -6718.448383
EM: Round [63] log likelihood: -6718.440083
EM: Round [64] log likelihood: -6718.432155
EM: Round [65] log likelihood: -6718.424580
EM: Round [66] log likelihood: -6718.417337
EM: Round [67] log likelihood: -6718.410409
EM: Round [68] log likelihood: -6718.403779
EM: Round [69] log likelihood: -6718.397432
EM: Round [70] log likelihood: -6718.391352
EM: Round [71] log likelihood: -6718.385526
EM: Round [72] log likelihood: -6718.379941
EM: Round [73] log likelihood: -6718.374586
EM: Round [74] log likelihood: -6718.369448
EM: Round [75] log likelihood: -6718.364517
EM: Round [76] log likelihood: -6718.359783
EM: Round [77] log likelihood: -6718.355237
EM: Round [78] log likelihood: -6718.350871
EM: Round [79] log likelihood: -6718.346675
EM: Round [80] log likelihood: -6718.342641
EM: Round [81] log likelihood: -6718.338764
EM: Round [82] log likelihood: -6718.335035
EM: Round [83] log likelihood: -6718.331447
EM: Round [84] log likelihood: -6718.327996
EM: Round [85] log likelihood: -6718.324674
EM: Round [86] log likelihood: -6718.321477
EM: Round [87] log likelihood: -6718.318398
EM: Round [88] log likelihood: -6718.315433
EM: Round [89] log likelihood: -6718.312578
EM: Round [90] log likelihood: -6718.309827
EM: Round [91] log likelihood: -6718.307177
EM: Round [92] log likelihood: -6718.304622
EM: Round [93] log likelihood: -6718.302161
EM: Round [94] log likelihood: -6718.299788
EM: Round [95] log likelihood: -6718.297500
EM: Round [96] log likelihood: -6718.295293
EM: Round [97] log likelihood: -6718.293166
EM: Round [98] log likelihood: -6718.291114
EM: Round [99] log likelihood: -6718.289134
EM: Round [100] log likelihood: -6718.287225
EM: Round [101] log likelihood: -6718.285383
EM: Round [102] log likelihood: -6718.283605
EM: Round [103] log likelihood: -6718.281889
EM: Round [104] log likelihood: -6718.280234
EM: Round [105] log likelihood: -6718.278636
EM: Round [106] log likelihood: -6718.277093
EM: Round [107] log likelihood: -6718.275604
EM: Round [108] log likelihood: -6718.274167
EM: Round [109] log likelihood: -6718.272779
EM: Round [110] log likelihood: -6718.271438
EM: Round [111] log likelihood: -6718.270144
EM: Round [112] log likelihood: -6718.268895
EM: Round [113] log likelihood: -6718.267688
EM: Round [114] log likelihood: -6718.266522
EM: Round [115] log likelihood: -6718.265397
EM: Round [116] log likelihood: -6718.264309
EM: Round [117] log likelihood: -6718.263259
EM: Round [118] log likelihood: -6718.262244
EM: Round [119] log likelihood: -6718.261264
EM: Round [120] log likelihood: -6718.260318
EM: Round [121] log likelihood: -6718.259403
EM: Round [122] log likelihood: -6718.258519
EM: Round [123] log likelihood: -6718.257665
EM: Round [124] log likelihood: -6718.256840
EM: Round [125] log likelihood: -6718.256043
EM: Round [126] log likelihood: -6718.255272
EM: Round [127] log likelihood: -6718.254528
EM: Round [128] log likelihood: -6718.253809
EM: Round [129] log likelihood: -6718.253114
EM: Round [130] log likelihood: -6718.252442
EM: Round [131] log likelihood: -6718.251793
EM: Round [132] log likelihood: -6718.251165
EM: Round [133] log likelihood: -6718.250559
EM: Round [134] log likelihood: -6718.249973
EM: Round [135] log likelihood: -6718.249407
EM: Round [136] log likelihood: -6718.248859
EM: Round [137] log likelihood: -6718.248330
EM: Round [138] log likelihood: -6718.247819
EM: Round [139] log likelihood: -6718.247325
EM: Round [140] log likelihood: -6718.246847
EM: Round [141] log likelihood: -6718.246385
EM: Round [142] log likelihood: -6718.245939
EM: Round [143] log likelihood: -6718.245507
EM: Round [144] log likelihood: -6718.245090
EM: Round [145] log likelihood: -6718.244687
EM: Round [146] log likelihood: -6718.244297
EM: Round [147] log likelihood: -6718.243920
EM: Round [148] log likelihood: -6718.243556
EM: Round [149] log likelihood: -6718.243204
EM: Round [150] log likelihood: -6718.242864
EM: Round [151] log likelihood: -6718.242535
EM: Round [152] log likelihood: -6718.242217
EM: Round [153] log likelihood: -6718.241909
EM: Round [154] log likelihood: -6718.241612
EM: Round [155] log likelihood: -6718.241325
EM: Round [156] log likelihood: -6718.241047
EM: Round [157] log likelihood: -6718.240778
EM: Round [158] log likelihood: -6718.240519
EM: Round [159] log likelihood: -6718.240268
EM: Round [160] log likelihood: -6718.240025
EM: Round [161] log likelihood: -6718.239791
EM: Round [162] log likelihood: -6718.239564
EM: Round [163] log likelihood: -6718.239344
EM: Round [164] log likelihood: -6718.239133
EM: Round [165] log likelihood: -6718.238928
EM: Round [166] log likelihood: -6718.238729
EM: Round [167] log likelihood: -6718.238538
EM: Round [168] log likelihood: -6718.238353
EM: Round [169] log likelihood: -6718.238174
EM: Round [170] log likelihood: -6718.238000
EM: Round [171] log likelihood: -6718.237833
EM: Round [172] log likelihood: -6718.237671
EM: Round [173] log likelihood: -6718.237515
EM: Round [174] log likelihood: -6718.237364
EM: Round [175] log likelihood: -6718.237217
EM: Round [176] log likelihood: -6718.237076
EM: Round [177] log likelihood: -6718.236939
EM: Round [178] log likelihood: -6718.236807
EM: Round [179] log likelihood: -6718.236679
EM: Round [180] log likelihood: -6718.236556
EM: Round [181] log likelihood: -6718.236436
EM: Round [182] log likelihood: -6718.236321
EM: Round [183] log likelihood: -6718.236209
EM: Round [184] log likelihood: -6718.236101
EM: Round [185] log likelihood: -6718.235997
EM: Round [186] log likelihood: -6718.235896
EM: Round [187] log likelihood: -6718.235798
EM: Stopping iterations at round 187 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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa > /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6126.398363
EM: Round [1] log likelihood: -6088.747135
EM: Round [2] log likelihood: -6078.663716
EM: Round [3] log likelihood: -6076.097955
EM: Round [4] log likelihood: -6075.507332
EM: Round [5] log likelihood: -6075.383649
EM: Round [6] log likelihood: -6075.359357
EM: Round [7] log likelihood: -6075.354747
EM: Round [8] log likelihood: -6075.353886
EM: Round [9] log likelihood: -6075.353726
EM: Round [10] log likelihood: -6075.353696
EM: Stopping iterations at round 10 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296543195
Execution Time = 5.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf > /tmp/nxf.bbugZeEaKv/fi_workdir/microH.dat
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.bbugZeEaKv/fi_workdir/microH.dat /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.bbugZeEaKv/fi_workdir/microH.dat /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bbugZeEaKv --json_outfile /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bbugZeEaKv --json_outfile /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1 --html_output /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-5519ab-R1_A23YTGFLT4_1 --html_output /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000226240.2]
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 [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 [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bbugZeEaKv/ctat_genome_lib_build_dir > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.bbugZeEaKv/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory