Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/ae7163f197220953927716a4ac9fea/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/3f13db9eaad2bcee8932771431f51b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/3f13db9eaad2bcee8932771431f51b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/18e10315feae60772f9ebcbd8d282e/659_epG-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/18e10315feae60772f9ebcbd8d282e/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_epG-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_epG-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/cytoBand.txt
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.3wPegTwVqQ/fi_workdir --reads "/tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:08:38 ..... started STAR run
Jun 08 10:08:38 ..... loading genome
Jun 08 10:10:26 ... generating Suffix Array index
Jun 08 10:14:15 ... completed Suffix Array index
Jun 08 10:14:15 ..... processing annotations GTF
Jun 08 10:14:16 ..... inserting junctions into the genome indices
Jun 08 10:15:17 ..... started mapping
Jun 08 11:26:27 ..... finished mapping
Jun 08 11:26:28 ..... started sorting BAM
Jun 08 11:26:31 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 77.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.3wPegTwVqQ/fi_workdir --reads "/tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:27:05 : INFO : Done.
Execution Time = 0.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[5640000] -done parsing /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 5,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 200,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 124,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 275,
'num genes matched < 2' => 62,
' ** passed ** ' => 92233,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'per_id < 96' => 16334,
'low complexity anchor region' => 224,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
'small anchor length' => 348,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 48,
'num_hits: 7 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 42,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 31220,
'seq-similar region overlap' => 435,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 45
};
-writing fusion junction support info.
Execution Time = 3.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[608000] -fusion SPANNING read extraction for scaff: MBOAT2--KIDINS220
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[83000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[179000] -fusion SPANNING read extraction for scaff: NTN1--MYH10
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[30000]
[31000]
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[37000]
[38000] -fusion SPANNING read extraction for scaff: PBX3--RGS9
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[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
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[6000]
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[30000]
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[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[30000]
[31000]
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[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[1000]
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[3000]
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[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[30000]
[31000]
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[40000]
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[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
[1000]
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[6000]
[7000]
[8000]
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[30000]
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[40000]
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[44000]
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[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
[1000]
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[30000]
[31000]
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[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
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[48000]
[49000]
[50000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
[1000]
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[7000]
[8000]
[9000]
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[18000]
[19000]
[20000]
[21000]
[22000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[6000]
[7000]
[8000]
[9000]
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[11000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
[1000]
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[4000]
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[7000]
[8000]
[9000]
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[11000]
[12000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
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[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
[1000]
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[7000]
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[9000]
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[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[11000]
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
[1000]
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[6000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
[1000]
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[5000]
[6000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[8000]
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[11000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
[1000]
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[7000]
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[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[7000]
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[9000]
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[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[11000]
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
[1000]
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[3000]
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[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
[1000]
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[5000]
[6000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[18000]
[19000]
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[21000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[8000]
[9000]
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[11000]
[12000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
[1000]
[2000]
[3000]
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[6000]
[7000]
[8000]
[9000]
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[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[22000]
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[25000]
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[27000]
[28000]
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[9000]
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[11000]
[12000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[6000]
[7000]
[8000]
[9000]
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[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[11000]
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
[1000]
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[6000]
[7000]
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[11000]
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[18000]
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[20000]
[21000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[3000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
[1000]
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[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
[1000]
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[6000]
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[8000]
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[11000]
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[18000]
[19000]
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[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
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[30000]
[31000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
[1000]
[2000]
[3000]
[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
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[17000]
[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
[1000]
[2000]
[3000]
[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
[1000]
[2000]
[3000]
[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[33000] -fusion SPANNING read extraction for scaff: PRKCA--QRICH2
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[67000] -fusion SPANNING read extraction for scaff: PTEN--RBM20
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[149000] -fusion SPANNING read extraction for scaff: QRICH2--ACTN1
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[41000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[1759000] -fusion SPANNING read extraction for scaff: TMPRSS2--ERG
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[26000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[184000] -fusion SPANNING read extraction for scaff: ZZEF1--PIK3R5
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[168000] -fusion SPANNING read extraction for scaff: ZZEF1--AC002091.1
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[178000] -fusion SPANNING read extraction for scaff: ZZEF1--NTN1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 30682,
'seq similar region alignment' => 125814
};
Execution Time = 8.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -76210.677926
EM: Round [1] log likelihood: -76186.606325
EM: Round [2] log likelihood: -76179.806826
EM: Round [3] log likelihood: -76174.211985
EM: Round [4] log likelihood: -76169.455397
EM: Round [5] log likelihood: -76165.327201
EM: Round [6] log likelihood: -76161.696940
EM: Round [7] log likelihood: -76158.478619
EM: Round [8] log likelihood: -76155.611999
EM: Round [9] log likelihood: -76153.052146
EM: Round [10] log likelihood: -76150.763469
EM: Round [11] log likelihood: -76148.716323
EM: Round [12] log likelihood: -76146.885074
EM: Round [13] log likelihood: -76145.247022
EM: Round [14] log likelihood: -76143.781785
EM: Round [15] log likelihood: -76142.470957
EM: Round [16] log likelihood: -76141.297885
EM: Round [17] log likelihood: -76140.247523
EM: Round [18] log likelihood: -76139.306315
EM: Round [19] log likelihood: -76138.462080
EM: Round [20] log likelihood: -76137.703912
EM: Round [21] log likelihood: -76137.022074
EM: Round [22] log likelihood: -76136.407900
EM: Round [23] log likelihood: -76135.853693
EM: Round [24] log likelihood: -76135.352631
EM: Round [25] log likelihood: -76134.898681
EM: Round [26] log likelihood: -76134.486511
EM: Round [27] log likelihood: -76134.111416
EM: Round [28] log likelihood: -76133.769248
EM: Round [29] log likelihood: -76133.456349
EM: Round [30] log likelihood: -76133.169499
EM: Round [31] log likelihood: -76132.905858
EM: Round [32] log likelihood: -76132.662927
EM: Round [33] log likelihood: -76132.438501
EM: Round [34] log likelihood: -76132.230638
EM: Round [35] log likelihood: -76132.037622
EM: Round [36] log likelihood: -76131.857942
EM: Round [37] log likelihood: -76131.690261
EM: Round [38] log likelihood: -76131.533396
EM: Round [39] log likelihood: -76131.386301
EM: Round [40] log likelihood: -76131.248050
EM: Round [41] log likelihood: -76131.117819
EM: Round [42] log likelihood: -76130.994878
EM: Round [43] log likelihood: -76130.878578
EM: Round [44] log likelihood: -76130.768339
EM: Round [45] log likelihood: -76130.663645
EM: Round [46] log likelihood: -76130.564035
EM: Round [47] log likelihood: -76130.469097
EM: Round [48] log likelihood: -76130.378459
EM: Round [49] log likelihood: -76130.291792
EM: Round [50] log likelihood: -76130.208795
EM: Round [51] log likelihood: -76130.129200
EM: Round [52] log likelihood: -76130.052764
EM: Round [53] log likelihood: -76129.979268
EM: Round [54] log likelihood: -76129.908513
EM: Round [55] log likelihood: -76129.840319
EM: Round [56] log likelihood: -76129.774521
EM: Round [57] log likelihood: -76129.710972
EM: Round [58] log likelihood: -76129.649534
EM: Round [59] log likelihood: -76129.590082
EM: Round [60] log likelihood: -76129.532504
EM: Round [61] log likelihood: -76129.476694
EM: Round [62] log likelihood: -76129.422556
EM: Round [63] log likelihood: -76129.370002
EM: Round [64] log likelihood: -76129.318950
EM: Round [65] log likelihood: -76129.269324
EM: Round [66] log likelihood: -76129.221054
EM: Round [67] log likelihood: -76129.174076
EM: Round [68] log likelihood: -76129.128329
EM: Round [69] log likelihood: -76129.083758
EM: Round [70] log likelihood: -76129.040309
EM: Round [71] log likelihood: -76128.997934
EM: Round [72] log likelihood: -76128.956588
EM: Round [73] log likelihood: -76128.916227
EM: Round [74] log likelihood: -76128.876812
EM: Round [75] log likelihood: -76128.838305
EM: Round [76] log likelihood: -76128.800671
EM: Round [77] log likelihood: -76128.763875
EM: Round [78] log likelihood: -76128.727888
EM: Round [79] log likelihood: -76128.692678
EM: Round [80] log likelihood: -76128.658218
EM: Round [81] log likelihood: -76128.624481
EM: Round [82] log likelihood: -76128.591442
EM: Round [83] log likelihood: -76128.559078
EM: Round [84] log likelihood: -76128.527365
EM: Round [85] log likelihood: -76128.496283
EM: Round [86] log likelihood: -76128.465809
EM: Round [87] log likelihood: -76128.435926
EM: Round [88] log likelihood: -76128.406614
EM: Round [89] log likelihood: -76128.377856
EM: Round [90] log likelihood: -76128.349634
EM: Round [91] log likelihood: -76128.321933
EM: Round [92] log likelihood: -76128.294737
EM: Round [93] log likelihood: -76128.268031
EM: Round [94] log likelihood: -76128.241801
EM: Round [95] log likelihood: -76128.216033
EM: Round [96] log likelihood: -76128.190715
EM: Round [97] log likelihood: -76128.165834
EM: Round [98] log likelihood: -76128.141378
EM: Round [99] log likelihood: -76128.117335
EM: Round [100] log likelihood: -76128.093694
EM: Round [101] log likelihood: -76128.070446
EM: Round [102] log likelihood: -76128.047579
EM: Round [103] log likelihood: -76128.025083
EM: Round [104] log likelihood: -76128.002950
EM: Round [105] log likelihood: -76127.981169
EM: Round [106] log likelihood: -76127.959733
EM: Round [107] log likelihood: -76127.938632
EM: Round [108] log likelihood: -76127.917859
EM: Round [109] log likelihood: -76127.897406
EM: Round [110] log likelihood: -76127.877265
EM: Round [111] log likelihood: -76127.857428
EM: Round [112] log likelihood: -76127.837889
EM: Round [113] log likelihood: -76127.818640
EM: Round [114] log likelihood: -76127.799676
EM: Round [115] log likelihood: -76127.780989
EM: Round [116] log likelihood: -76127.762573
EM: Round [117] log likelihood: -76127.744422
EM: Round [118] log likelihood: -76127.726531
EM: Round [119] log likelihood: -76127.708894
EM: Round [120] log likelihood: -76127.691505
EM: Round [121] log likelihood: -76127.674360
EM: Round [122] log likelihood: -76127.657452
EM: Round [123] log likelihood: -76127.640777
EM: Round [124] log likelihood: -76127.624330
EM: Round [125] log likelihood: -76127.608106
EM: Round [126] log likelihood: -76127.592101
EM: Round [127] log likelihood: -76127.576311
EM: Round [128] log likelihood: -76127.560730
EM: Round [129] log likelihood: -76127.545356
EM: Round [130] log likelihood: -76127.530183
EM: Round [131] log likelihood: -76127.515209
EM: Round [132] log likelihood: -76127.500428
EM: Round [133] log likelihood: -76127.485838
EM: Round [134] log likelihood: -76127.471435
EM: Round [135] log likelihood: -76127.457215
EM: Round [136] log likelihood: -76127.443174
EM: Round [137] log likelihood: -76127.429311
EM: Round [138] log likelihood: -76127.415620
EM: Round [139] log likelihood: -76127.402099
EM: Round [140] log likelihood: -76127.388746
EM: Round [141] log likelihood: -76127.375556
EM: Round [142] log likelihood: -76127.362528
EM: Round [143] log likelihood: -76127.349658
EM: Round [144] log likelihood: -76127.336943
EM: Round [145] log likelihood: -76127.324381
EM: Round [146] log likelihood: -76127.311969
EM: Round [147] log likelihood: -76127.299705
EM: Round [148] log likelihood: -76127.287585
EM: Round [149] log likelihood: -76127.275608
EM: Round [150] log likelihood: -76127.263772
EM: Round [151] log likelihood: -76127.252073
EM: Round [152] log likelihood: -76127.240510
EM: Round [153] log likelihood: -76127.229080
EM: Round [154] log likelihood: -76127.217781
EM: Round [155] log likelihood: -76127.206611
EM: Round [156] log likelihood: -76127.195569
EM: Round [157] log likelihood: -76127.184651
EM: Round [158] log likelihood: -76127.173856
EM: Round [159] log likelihood: -76127.163182
EM: Round [160] log likelihood: -76127.152627
EM: Round [161] log likelihood: -76127.142190
EM: Round [162] log likelihood: -76127.131868
EM: Round [163] log likelihood: -76127.121659
EM: Round [164] log likelihood: -76127.111563
EM: Round [165] log likelihood: -76127.101577
EM: Round [166] log likelihood: -76127.091699
EM: Round [167] log likelihood: -76127.081929
EM: Round [168] log likelihood: -76127.072263
EM: Round [169] log likelihood: -76127.062702
EM: Round [170] log likelihood: -76127.053243
EM: Round [171] log likelihood: -76127.043884
EM: Round [172] log likelihood: -76127.034625
EM: Round [173] log likelihood: -76127.025464
EM: Round [174] log likelihood: -76127.016399
EM: Round [175] log likelihood: -76127.007429
EM: Round [176] log likelihood: -76126.998554
EM: Round [177] log likelihood: -76126.989770
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EM: Round [639] log likelihood: -76125.987700
EM: Round [640] log likelihood: -76125.987435
EM: Round [641] log likelihood: -76125.987172
EM: Round [642] log likelihood: -76125.986911
EM: Round [643] log likelihood: -76125.986651
EM: Round [644] log likelihood: -76125.986393
EM: Round [645] log likelihood: -76125.986137
EM: Round [646] log likelihood: -76125.985882
EM: Round [647] log likelihood: -76125.985629
EM: Round [648] log likelihood: -76125.985378
EM: Round [649] log likelihood: -76125.985129
EM: Round [650] log likelihood: -76125.984881
EM: Round [651] log likelihood: -76125.984635
EM: Round [652] log likelihood: -76125.984390
EM: Round [653] log likelihood: -76125.984148
EM: Round [654] log likelihood: -76125.983906
EM: Round [655] log likelihood: -76125.983667
EM: Round [656] log likelihood: -76125.983429
EM: Round [657] log likelihood: -76125.983193
EM: Round [658] log likelihood: -76125.982958
EM: Round [659] log likelihood: -76125.982725
EM: Round [660] log likelihood: -76125.982493
EM: Round [661] log likelihood: -76125.982263
EM: Round [662] log likelihood: -76125.982034
EM: Round [663] log likelihood: -76125.981807
EM: Round [664] log likelihood: -76125.981582
EM: Round [665] log likelihood: -76125.981358
EM: Round [666] log likelihood: -76125.981135
EM: Round [667] log likelihood: -76125.980914
EM: Round [668] log likelihood: -76125.980695
EM: Round [669] log likelihood: -76125.980477
EM: Round [670] log likelihood: -76125.980260
EM: Round [671] log likelihood: -76125.980045
EM: Round [672] log likelihood: -76125.979831
EM: Round [673] log likelihood: -76125.979619
EM: Round [674] log likelihood: -76125.979408
EM: Round [675] log likelihood: -76125.979199
EM: Round [676] log likelihood: -76125.978991
EM: Round [677] log likelihood: -76125.978784
EM: Round [678] log likelihood: -76125.978579
EM: Round [679] log likelihood: -76125.978375
EM: Round [680] log likelihood: -76125.978173
EM: Round [681] log likelihood: -76125.977972
EM: Round [682] log likelihood: -76125.977772
EM: Round [683] log likelihood: -76125.977573
EM: Round [684] log likelihood: -76125.977376
EM: Round [685] log likelihood: -76125.977180
EM: Round [686] log likelihood: -76125.976986
EM: Round [687] log likelihood: -76125.976793
EM: Round [688] log likelihood: -76125.976601
EM: Round [689] log likelihood: -76125.976410
EM: Round [690] log likelihood: -76125.976221
EM: Round [691] log likelihood: -76125.976033
EM: Round [692] log likelihood: -76125.975846
EM: Round [693] log likelihood: -76125.975660
EM: Round [694] log likelihood: -76125.975476
EM: Round [695] log likelihood: -76125.975293
EM: Round [696] log likelihood: -76125.975111
EM: Round [697] log likelihood: -76125.974930
EM: Round [698] log likelihood: -76125.974751
EM: Round [699] log likelihood: -76125.974573
EM: Round [700] log likelihood: -76125.974396
EM: Round [701] log likelihood: -76125.974220
EM: Round [702] log likelihood: -76125.974045
EM: Round [703] log likelihood: -76125.973871
EM: Round [704] log likelihood: -76125.973699
EM: Round [705] log likelihood: -76125.973528
EM: Round [706] log likelihood: -76125.973358
EM: Round [707] log likelihood: -76125.973189
EM: Round [708] log likelihood: -76125.973021
EM: Round [709] log likelihood: -76125.972854
EM: Round [710] log likelihood: -76125.972689
EM: Round [711] log likelihood: -76125.972524
EM: Round [712] log likelihood: -76125.972361
EM: Round [713] log likelihood: -76125.972199
EM: Round [714] log likelihood: -76125.972037
EM: Round [715] log likelihood: -76125.971877
EM: Round [716] log likelihood: -76125.971718
EM: Round [717] log likelihood: -76125.971560
EM: Round [718] log likelihood: -76125.971403
EM: Round [719] log likelihood: -76125.971247
EM: Round [720] log likelihood: -76125.971093
EM: Round [721] log likelihood: -76125.970939
EM: Round [722] log likelihood: -76125.970786
EM: Round [723] log likelihood: -76125.970634
EM: Round [724] log likelihood: -76125.970483
EM: Round [725] log likelihood: -76125.970334
EM: Round [726] log likelihood: -76125.970185
EM: Round [727] log likelihood: -76125.970037
EM: Round [728] log likelihood: -76125.969890
EM: Round [729] log likelihood: -76125.969745
EM: Round [730] log likelihood: -76125.969600
EM: Round [731] log likelihood: -76125.969456
EM: Round [732] log likelihood: -76125.969313
EM: Round [733] log likelihood: -76125.969171
EM: Round [734] log likelihood: -76125.969030
EM: Round [735] log likelihood: -76125.968890
EM: Round [736] log likelihood: -76125.968751
EM: Round [737] log likelihood: -76125.968613
EM: Round [738] log likelihood: -76125.968476
EM: Round [739] log likelihood: -76125.968339
EM: Round [740] log likelihood: -76125.968204
EM: Round [741] log likelihood: -76125.968069
EM: Round [742] log likelihood: -76125.967936
EM: Round [743] log likelihood: -76125.967803
EM: Round [744] log likelihood: -76125.967671
EM: Round [745] log likelihood: -76125.967540
EM: Round [746] log likelihood: -76125.967410
EM: Round [747] log likelihood: -76125.967281
EM: Round [748] log likelihood: -76125.967152
EM: Round [749] log likelihood: -76125.967025
EM: Round [750] log likelihood: -76125.966898
EM: Round [751] log likelihood: -76125.966772
EM: Round [752] log likelihood: -76125.966647
EM: Round [753] log likelihood: -76125.966523
EM: Round [754] log likelihood: -76125.966400
EM: Round [755] log likelihood: -76125.966277
EM: Round [756] log likelihood: -76125.966156
EM: Round [757] log likelihood: -76125.966035
EM: Round [758] log likelihood: -76125.965915
EM: Round [759] log likelihood: -76125.965796
EM: Round [760] log likelihood: -76125.965677
EM: Round [761] log likelihood: -76125.965559
EM: Round [762] log likelihood: -76125.965443
EM: Round [763] log likelihood: -76125.965326
EM: Round [764] log likelihood: -76125.965211
EM: Round [765] log likelihood: -76125.965097
EM: Round [766] log likelihood: -76125.964983
EM: Round [767] log likelihood: -76125.964870
EM: Round [768] log likelihood: -76125.964757
EM: Round [769] log likelihood: -76125.964646
EM: Round [770] log likelihood: -76125.964535
EM: Round [771] log likelihood: -76125.964425
EM: Round [772] log likelihood: -76125.964316
EM: Round [773] log likelihood: -76125.964207
EM: Round [774] log likelihood: -76125.964099
EM: Round [775] log likelihood: -76125.963992
EM: Round [776] log likelihood: -76125.963886
EM: Round [777] log likelihood: -76125.963780
EM: Round [778] log likelihood: -76125.963675
EM: Round [779] log likelihood: -76125.963570
EM: Round [780] log likelihood: -76125.963467
EM: Round [781] log likelihood: -76125.963364
EM: Round [782] log likelihood: -76125.963262
EM: Round [783] log likelihood: -76125.963160
EM: Round [784] log likelihood: -76125.963059
EM: Round [785] log likelihood: -76125.962959
EM: Round [786] log likelihood: -76125.962859
EM: Stopping iterations at round 786 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/659_epG-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -71928.906967
EM: Round [1] log likelihood: -71928.667971
EM: Round [2] log likelihood: -71928.667942
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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295912345
Execution Time = 5.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.3wPegTwVqQ/fi_workdir/microH.dat
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.3wPegTwVqQ/fi_workdir/microH.dat /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/microH.dat /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3wPegTwVqQ --json_outfile /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3wPegTwVqQ --json_outfile /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_epG-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000225470.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3wPegTwVqQ/ctat_genome_lib_build_dir > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.3wPegTwVqQ/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory