Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/c9cffc217fbdb01de2b1ab56b85209/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/9a83d1833bc71f1fedeff4a3f74308/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/af22d4353f11435af0719d8626e376/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/af22d4353f11435af0719d8626e376/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/c9cffc217fbdb01de2b1ab56b85209/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --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 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/cytoBand.txt
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fRn8usSdjx/fi_workdir --reads "/tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:50:42 ..... started STAR run
Jun 08 09:50:42 ..... loading genome
Jun 08 09:52:31 ... generating Suffix Array index
Jun 08 09:57:08 ... completed Suffix Array index
Jun 08 09:57:09 ..... processing annotations GTF
Jun 08 09:57:09 ..... inserting junctions into the genome indices
Jun 08 09:58:11 ..... started mapping
Jun 08 10:41:54 ..... finished mapping
Jun 08 10:41:55 ..... started sorting BAM
Jun 08 10:42:00 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 51.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fRn8usSdjx/fi_workdir --reads "/tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
10:42:56 : INFO : Done.
Execution Time = 0.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.11 minutes. CMD: samtools index /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[11020000] -done parsing /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 47283,
'num genes matched < 2' => 46,
'small anchor length' => 52,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 548,
'excessive soft clipping' => 98265,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 44,
'seq-similar region overlap' => 48,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 56,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 81,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 216,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'exons hit < 2' => 41,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 44,
' ** passed ** ' => 72241,
'low complexity anchor region' => 537,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 5,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 15
};
-writing fusion junction support info.
Execution Time = 6.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[143000] -fusion SPANNING read extraction for scaff: AC005670.3--KANSL1
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[43000] -fusion SPANNING read extraction for scaff: AC015712.1--FAM13C
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[1180000] -fusion SPANNING read extraction for scaff: AC090197.1--NKX3-1
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[118000] -fusion SPANNING read extraction for scaff: ACAD11--RN7SL300P
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[118000] -fusion SPANNING read extraction for scaff: ACAD11--AC078788.1
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[18000] -fusion SPANNING read extraction for scaff: ACBD5--AL356157.2
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[16000] -fusion SPANNING read extraction for scaff: ACBD5--AL356157.3
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[17000] -fusion SPANNING read extraction for scaff: AGTR1--RNA5SP144
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[17000] -fusion SPANNING read extraction for scaff: AGTR1--AC011592.1
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[17000] -fusion SPANNING read extraction for scaff: AGTR1--LARP7P4
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[63000] -fusion SPANNING read extraction for scaff: AKAP1--DLL4
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[15000] -fusion SPANNING read extraction for scaff: ALS2CL--PRSS46P
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[40000] -fusion SPANNING read extraction for scaff: ANKRD28--AC092957.1
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[30000] -fusion SPANNING read extraction for scaff: ARHGEF26--LINC00882
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[1226000] -fusion SPANNING read extraction for scaff: LOXL2--NKX3-1
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[246000] -fusion SPANNING read extraction for scaff: MAGI1--LRIG1
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[94000] -fusion SPANNING read extraction for scaff: MAGI1--AC104440.1
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[249000] -fusion SPANNING read extraction for scaff: MAML3--TBC1D9
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[94000] -fusion SPANNING read extraction for scaff: MBNL1--RAP1BP2
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[95000] -fusion SPANNING read extraction for scaff: MBNL1--AC091804.1
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[43000] -fusion SPANNING read extraction for scaff: MEGF9--PHF19
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[61000] -fusion SPANNING read extraction for scaff: MOSPD3--PSMD8
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[75000] -fusion SPANNING read extraction for scaff: NAALADL2--PIK3CB
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[16000] -fusion SPANNING read extraction for scaff: NECTIN3--RNU6-138P
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[18000] -fusion SPANNING read extraction for scaff: NECTIN3--KCNH8
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[56000] -fusion SPANNING read extraction for scaff: NUAK2--NUCKS1
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[26000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[28000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[35000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[12000] -fusion SPANNING read extraction for scaff: PCMT1--KIF20B
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[23000] -fusion SPANNING read extraction for scaff: PIK3R4--NLGN1
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[22000] -fusion SPANNING read extraction for scaff: PLOD2--AC011592.1
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[22000] -fusion SPANNING read extraction for scaff: PLOD2--LARP7P4
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[52000] -fusion SPANNING read extraction for scaff: PPA2--INTS12
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[42000] -fusion SPANNING read extraction for scaff: PPA2--GSTCD
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[42000] -fusion SPANNING read extraction for scaff: PRRC1--AC034206.1
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[43000] -fusion SPANNING read extraction for scaff: PRRC1--SLC25A48
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[32000] -fusion SPANNING read extraction for scaff: PRRC1--AC022513.1
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[32000] -fusion SPANNING read extraction for scaff: PRRC1--LINC01479
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[58000] -fusion SPANNING read extraction for scaff: PSMD8--TFR2
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[92000] -fusion SPANNING read extraction for scaff: RBBP4--FAM13C
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[127000] -fusion SPANNING read extraction for scaff: RGL3--DOCK6
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[28000] -fusion SPANNING read extraction for scaff: ROBO1--CMSS1
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[25000] -fusion SPANNING read extraction for scaff: RSRC1--LMCD1
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[309000] -fusion SPANNING read extraction for scaff: SERINC5--AC090709.1
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[310000] -fusion SPANNING read extraction for scaff: SERINC5--SYT1
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[125000] -fusion SPANNING read extraction for scaff: SF3A1--KANSL1
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[1324000] -fusion SPANNING read extraction for scaff: SND1--AC000124.1
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[21000] -fusion SPANNING read extraction for scaff: STAG1--GSTO3P
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[92000] -fusion SPANNING read extraction for scaff: STAG1--ATP2C1
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[150000] -fusion SPANNING read extraction for scaff: TANC1--AC079150.1
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[150000] -fusion SPANNING read extraction for scaff: TANC1--LINC01850
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[53000] -fusion SPANNING read extraction for scaff: TBL1XR1--LINC01208
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[52000] -fusion SPANNING read extraction for scaff: TBL1XR1--MTND5P15
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[34000] -fusion SPANNING read extraction for scaff: TCTN1--TOR1AIP2
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[12000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[62000] -fusion SPANNING read extraction for scaff: XRN1--ARPP21
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[75000] -fusion SPANNING read extraction for scaff: ZNF148--CPB1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 19866,
'lacks exon overlap' => 88727
};
Execution Time = 15.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -54325.114880
EM: Round [1] log likelihood: -54324.948255
EM: Round [2] log likelihood: -54324.917693
EM: Round [3] log likelihood: -54324.889084
EM: Round [4] log likelihood: -54324.862250
EM: Round [5] log likelihood: -54324.837039
EM: Round [6] log likelihood: -54324.813316
EM: Round [7] log likelihood: -54324.790961
EM: Round [8] log likelihood: -54324.769868
EM: Round [9] log likelihood: -54324.749941
EM: Round [10] log likelihood: -54324.731095
EM: Round [11] log likelihood: -54324.713252
EM: Round [12] log likelihood: -54324.696342
EM: Round [13] log likelihood: -54324.680303
EM: Round [14] log likelihood: -54324.665077
EM: Round [15] log likelihood: -54324.650611
EM: Round [16] log likelihood: -54324.636857
EM: Round [17] log likelihood: -54324.623770
EM: Round [18] log likelihood: -54324.611312
EM: Round [19] log likelihood: -54324.599443
EM: Round [20] log likelihood: -54324.588131
EM: Round [21] log likelihood: -54324.577342
EM: Round [22] log likelihood: -54324.567048
EM: Round [23] log likelihood: -54324.557220
EM: Round [24] log likelihood: -54324.547834
EM: Round [25] log likelihood: -54324.538867
EM: Round [26] log likelihood: -54324.530294
EM: Round [27] log likelihood: -54324.522097
EM: Round [28] log likelihood: -54324.514256
EM: Round [29] log likelihood: -54324.506753
EM: Round [30] log likelihood: -54324.499571
EM: Round [31] log likelihood: -54324.492693
EM: Round [32] log likelihood: -54324.486106
EM: Round [33] log likelihood: -54324.479795
EM: Round [34] log likelihood: -54324.473747
EM: Round [35] log likelihood: -54324.467949
EM: Round [36] log likelihood: -54324.462390
EM: Round [37] log likelihood: -54324.457059
EM: Round [38] log likelihood: -54324.451944
EM: Round [39] log likelihood: -54324.447038
EM: Round [40] log likelihood: -54324.442329
EM: Round [41] log likelihood: -54324.437809
EM: Round [42] log likelihood: -54324.433469
EM: Round [43] log likelihood: -54324.429303
EM: Round [44] log likelihood: -54324.425302
EM: Round [45] log likelihood: -54324.421458
EM: Round [46] log likelihood: -54324.417766
EM: Round [47] log likelihood: -54324.414219
EM: Round [48] log likelihood: -54324.410810
EM: Round [49] log likelihood: -54324.407534
EM: Round [50] log likelihood: -54324.404385
EM: Round [51] log likelihood: -54324.401358
EM: Round [52] log likelihood: -54324.398448
EM: Round [53] log likelihood: -54324.395649
EM: Round [54] log likelihood: -54324.392958
EM: Round [55] log likelihood: -54324.390370
EM: Round [56] log likelihood: -54324.387880
EM: Round [57] log likelihood: -54324.385486
EM: Round [58] log likelihood: -54324.383182
EM: Round [59] log likelihood: -54324.380966
EM: Round [60] log likelihood: -54324.378833
EM: Round [61] log likelihood: -54324.376781
EM: Round [62] log likelihood: -54324.374806
EM: Round [63] log likelihood: -54324.372906
EM: Round [64] log likelihood: -54324.371076
EM: Round [65] log likelihood: -54324.369315
EM: Round [66] log likelihood: -54324.367620
EM: Round [67] log likelihood: -54324.365989
EM: Round [68] log likelihood: -54324.364418
EM: Round [69] log likelihood: -54324.362905
EM: Round [70] log likelihood: -54324.361449
EM: Round [71] log likelihood: -54324.360046
EM: Round [72] log likelihood: -54324.358696
EM: Round [73] log likelihood: -54324.357396
EM: Round [74] log likelihood: -54324.356143
EM: Round [75] log likelihood: -54324.354937
EM: Round [76] log likelihood: -54324.353775
EM: Round [77] log likelihood: -54324.352656
EM: Round [78] log likelihood: -54324.351578
EM: Round [79] log likelihood: -54324.350540
EM: Round [80] log likelihood: -54324.349540
EM: Round [81] log likelihood: -54324.348577
EM: Round [82] log likelihood: -54324.347648
EM: Round [83] log likelihood: -54324.346754
EM: Round [84] log likelihood: -54324.345893
EM: Round [85] log likelihood: -54324.345063
EM: Round [86] log likelihood: -54324.344263
EM: Round [87] log likelihood: -54324.343492
EM: Round [88] log likelihood: -54324.342750
EM: Round [89] log likelihood: -54324.342034
EM: Round [90] log likelihood: -54324.341345
EM: Round [91] log likelihood: -54324.340681
EM: Round [92] log likelihood: -54324.340040
EM: Round [93] log likelihood: -54324.339424
EM: Round [94] log likelihood: -54324.338829
EM: Round [95] log likelihood: -54324.338256
EM: Round [96] log likelihood: -54324.337704
EM: Round [97] log likelihood: -54324.337172
EM: Round [98] log likelihood: -54324.336659
EM: Round [99] log likelihood: -54324.336164
EM: Round [100] log likelihood: -54324.335688
EM: Round [101] log likelihood: -54324.335229
EM: Round [102] log likelihood: -54324.334786
EM: Round [103] log likelihood: -54324.334359
EM: Round [104] log likelihood: -54324.333948
EM: Round [105] log likelihood: -54324.333552
EM: Round [106] log likelihood: -54324.333170
EM: Round [107] log likelihood: -54324.332801
EM: Round [108] log likelihood: -54324.332446
EM: Round [109] log likelihood: -54324.332104
EM: Round [110] log likelihood: -54324.331774
EM: Round [111] log likelihood: -54324.331456
EM: Round [112] log likelihood: -54324.331150
EM: Round [113] log likelihood: -54324.330854
EM: Round [114] log likelihood: -54324.330569
EM: Round [115] log likelihood: -54324.330295
EM: Round [116] log likelihood: -54324.330030
EM: Round [117] log likelihood: -54324.329775
EM: Round [118] log likelihood: -54324.329529
EM: Round [119] log likelihood: -54324.329291
EM: Round [120] log likelihood: -54324.329063
EM: Round [121] log likelihood: -54324.328842
EM: Round [122] log likelihood: -54324.328630
EM: Round [123] log likelihood: -54324.328425
EM: Round [124] log likelihood: -54324.328227
EM: Round [125] log likelihood: -54324.328037
EM: Round [126] log likelihood: -54324.327853
EM: Round [127] log likelihood: -54324.327676
EM: Round [128] log likelihood: -54324.327505
EM: Round [129] log likelihood: -54324.327341
EM: Round [130] log likelihood: -54324.327182
EM: Round [131] log likelihood: -54324.327029
EM: Round [132] log likelihood: -54324.326882
EM: Round [133] log likelihood: -54324.326740
EM: Round [134] log likelihood: -54324.326602
EM: Round [135] log likelihood: -54324.326470
EM: Round [136] log likelihood: -54324.326343
EM: Round [137] log likelihood: -54324.326220
EM: Round [138] log likelihood: -54324.326102
EM: Round [139] log likelihood: -54324.325987
EM: Round [140] log likelihood: -54324.325877
EM: Round [141] log likelihood: -54324.325771
EM: Round [142] log likelihood: -54324.325669
EM: Round [143] log likelihood: -54324.325570
EM: Stopping iterations at round 143 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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.10 minutes. CMD: samtools index /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 2.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir
-done, see /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -52817.229717
EM: Round [1] log likelihood: -52817.193975
EM: Round [2] log likelihood: -52817.193974
EM: Stopping iterations at round 2 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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 239256955
Execution Time = 4.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fRn8usSdjx/fi_workdir/microH.dat
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.fRn8usSdjx/fi_workdir/microH.dat /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.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.fRn8usSdjx/fi_workdir/microH.dat /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fRn8usSdjx --json_outfile /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fRn8usSdjx --json_outfile /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.fRn8usSdjx/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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.05 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.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000226770.1]
WARNING, no entry stored in dbm for [ENSG00000223715.3]
WARNING, no entry stored in dbm for [ENSG00000223715.3]
WARNING, no entry stored in dbm for [ENSG00000223715.3]
WARNING, no entry stored in dbm for [ENSG00000223715.3]
WARNING, no entry stored in dbm for [ENSG00000240541.3]
WARNING, no entry stored in dbm for [ENSG00000240541.3]
WARNING, no entry stored in dbm for [ENSG00000240541.3]
WARNING, no entry stored in dbm for [ENSG00000240541.3]
WARNING, no entry stored in dbm for [ENSG00000240541.3]
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 [ENSG00000257191.1]
WARNING, no entry stored in dbm for [ENSG00000257191.1]
WARNING, no entry stored in dbm for [ENSG00000243620.2]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000250167.1]
WARNING, no entry stored in dbm for [ENSG00000261603.3]
WARNING, no entry stored in dbm for [ENSG00000286712.1]
WARNING, no entry stored in dbm for [ENSG00000179141.9]
WARNING, no entry stored in dbm for [ENSG00000179141.9]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000225470.8]
WARNING, no entry stored in dbm for [ENSG00000270767.1]
WARNING, no entry stored in dbm for [ENSG00000237424.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fRn8usSdjx/ctat_genome_lib_build_dir > /tmp/nxf.fRn8usSdjx/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.fRn8usSdjx/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory