Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/1a0c331f35208e7e3385fce5b682e7/659_bjQ-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/69/ef4302d3f83e508ecd1622453e2445/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/dea2b1f56c72a1cb899cadf5ac93b8/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/ef4302d3f83e508ecd1622453e2445/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/dea2b1f56c72a1cb899cadf5ac93b8/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/cytoBand.txt
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.JjpTaMw6Cs/fi_workdir --reads "/tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:14:53 ..... started STAR run
Jun 08 10:14:53 ..... loading genome
Jun 08 10:16:48 ... generating Suffix Array index
Jun 08 10:20:59 ... completed Suffix Array index
Jun 08 10:20:59 ..... processing annotations GTF
Jun 08 10:20:59 ..... inserting junctions into the genome indices
Jun 08 10:22:06 ..... started mapping
Jun 08 11:46:22 ..... finished mapping
Jun 08 11:46:25 ..... started sorting BAM
Jun 08 11:46:27 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 91.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.JjpTaMw6Cs/fi_workdir --reads "/tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:46:58 : INFO : Done.
Execution Time = 0.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[5090000] -done parsing /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 6685,
'small anchor length' => 57,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 24,
'exons hit < 2' => 14,
'num genes matched < 2' => 27,
'seq-similar region overlap' => 3,
'low complexity anchor region' => 13,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 19,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 236,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2940,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1676,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 796,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 72,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 381,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 12,
' ** passed ** ' => 10787,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 2091,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 174,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 28,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 912,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 768,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 750,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'per_id < 96' => 39969,
'excessive soft clipping' => 61537,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 136,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2048
};
-writing fusion junction support info.
Execution Time = 2.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[23000] -fusion SPANNING read extraction for scaff: ABCC4--RNY4P27
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[22000] -fusion SPANNING read extraction for scaff: AC091132.4--AC091132.1
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[8000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[649000] -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12
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[72000] -fusion SPANNING read extraction for scaff: GLI3--AF246928.1
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[72000] -fusion SPANNING read extraction for scaff: GLI3--AJ009632.2
[1000] -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L
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[58000] -fusion SPANNING read extraction for scaff: GUSBP13--NAIP
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[356000] -fusion SPANNING read extraction for scaff: KIF5B--RET
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[5000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[110000] -fusion SPANNING read extraction for scaff: MCM3AP--MTRNR2L12
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[168000] -fusion SPANNING read extraction for scaff: NOLC1--GBF1
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[40000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[680000] -fusion SPANNING read extraction for scaff: PTPN2--NPIPB12
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[28000] -fusion SPANNING read extraction for scaff: RITA1--GLT8D2
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[23000] -fusion SPANNING read extraction for scaff: RPSAP52--HMGA2
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[87000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[58000] -fusion SPANNING read extraction for scaff: TAF4--AC114498.1
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[45000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[48000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[27000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 38354,
'seq similar region alignment' => 15577
};
Execution Time = 6.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7385.503179
EM: Round [1] log likelihood: -7380.744081
EM: Round [2] log likelihood: -7380.636381
EM: Round [3] log likelihood: -7380.615102
EM: Round [4] log likelihood: -7380.607357
EM: Round [5] log likelihood: -7380.602942
EM: Round [6] log likelihood: -7380.599381
EM: Round [7] log likelihood: -7380.596053
EM: Round [8] log likelihood: -7380.592806
EM: Round [9] log likelihood: -7380.589598
EM: Round [10] log likelihood: -7380.586422
EM: Round [11] log likelihood: -7380.583273
EM: Round [12] log likelihood: -7380.580151
EM: Round [13] log likelihood: -7380.577056
EM: Round [14] log likelihood: -7380.573987
EM: Round [15] log likelihood: -7380.570945
EM: Round [16] log likelihood: -7380.567928
EM: Round [17] log likelihood: -7380.564936
EM: Round [18] log likelihood: -7380.561970
EM: Round [19] log likelihood: -7380.559029
EM: Round [20] log likelihood: -7380.556112
EM: Round [21] log likelihood: -7380.553221
EM: Round [22] log likelihood: -7380.550353
EM: Round [23] log likelihood: -7380.547509
EM: Round [24] log likelihood: -7380.544690
EM: Round [25] log likelihood: -7380.541894
EM: Round [26] log likelihood: -7380.539121
EM: Round [27] log likelihood: -7380.536371
EM: Round [28] log likelihood: -7380.533645
EM: Round [29] log likelihood: -7380.530941
EM: Round [30] log likelihood: -7380.528259
EM: Round [31] log likelihood: -7380.525600
EM: Round [32] log likelihood: -7380.522962
EM: Round [33] log likelihood: -7380.520347
EM: Round [34] log likelihood: -7380.517753
EM: Round [35] log likelihood: -7380.515181
EM: Round [36] log likelihood: -7380.512629
EM: Round [37] log likelihood: -7380.510099
EM: Round [38] log likelihood: -7380.507590
EM: Round [39] log likelihood: -7380.505101
EM: Round [40] log likelihood: -7380.502632
EM: Round [41] log likelihood: -7380.500184
EM: Round [42] log likelihood: -7380.497756
EM: Round [43] log likelihood: -7380.495348
EM: Round [44] log likelihood: -7380.492959
EM: Round [45] log likelihood: -7380.490590
EM: Round [46] log likelihood: -7380.488240
EM: Round [47] log likelihood: -7380.485910
EM: Round [48] log likelihood: -7380.483598
EM: Round [49] log likelihood: -7380.481305
EM: Round [50] log likelihood: -7380.479030
EM: Round [51] log likelihood: -7380.476774
EM: Round [52] log likelihood: -7380.474537
EM: Round [53] log likelihood: -7380.472317
EM: Round [54] log likelihood: -7380.470115
EM: Round [55] log likelihood: -7380.467931
EM: Round [56] log likelihood: -7380.465765
EM: Round [57] log likelihood: -7380.463616
EM: Round [58] log likelihood: -7380.461484
EM: Round [59] log likelihood: -7380.459370
EM: Round [60] log likelihood: -7380.457272
EM: Round [61] log likelihood: -7380.455191
EM: Round [62] log likelihood: -7380.453127
EM: Round [63] log likelihood: -7380.451079
EM: Round [64] log likelihood: -7380.449048
EM: Round [65] log likelihood: -7380.447033
EM: Round [66] log likelihood: -7380.445034
EM: Round [67] log likelihood: -7380.443051
EM: Round [68] log likelihood: -7380.441084
EM: Round [69] log likelihood: -7380.439132
EM: Round [70] log likelihood: -7380.437196
EM: Round [71] log likelihood: -7380.435275
EM: Round [72] log likelihood: -7380.433370
EM: Round [73] log likelihood: -7380.431479
EM: Round [74] log likelihood: -7380.429604
EM: Round [75] log likelihood: -7380.427743
EM: Round [76] log likelihood: -7380.425897
EM: Round [77] log likelihood: -7380.424066
EM: Round [78] log likelihood: -7380.422249
EM: Round [79] log likelihood: -7380.420446
EM: Round [80] log likelihood: -7380.418658
EM: Round [81] log likelihood: -7380.416883
EM: Round [82] log likelihood: -7380.415123
EM: Round [83] log likelihood: -7380.413376
EM: Round [84] log likelihood: -7380.411643
EM: Round [85] log likelihood: -7380.409924
EM: Round [86] log likelihood: -7380.408218
EM: Round [87] log likelihood: -7380.406525
EM: Round [88] log likelihood: -7380.404846
EM: Round [89] log likelihood: -7380.403180
EM: Round [90] log likelihood: -7380.401527
EM: Round [91] log likelihood: -7380.399886
EM: Round [92] log likelihood: -7380.398259
EM: Round [93] log likelihood: -7380.396644
EM: Round [94] log likelihood: -7380.395042
EM: Round [95] log likelihood: -7380.393452
EM: Round [96] log likelihood: -7380.391874
EM: Round [97] log likelihood: -7380.390309
EM: Round [98] log likelihood: -7380.388756
EM: Round [99] log likelihood: -7380.387215
EM: Round [100] log likelihood: -7380.385686
EM: Round [101] log likelihood: -7380.384168
EM: Round [102] log likelihood: -7380.382663
EM: Round [103] log likelihood: -7380.381169
EM: Round [104] log likelihood: -7380.379686
EM: Round [105] log likelihood: -7380.378215
EM: Round [106] log likelihood: -7380.376756
EM: Round [107] log likelihood: -7380.375307
EM: Round [108] log likelihood: -7380.373870
EM: Round [109] log likelihood: -7380.372444
EM: Round [110] log likelihood: -7380.371029
EM: Round [111] log likelihood: -7380.369624
EM: Round [112] log likelihood: -7380.368231
EM: Round [113] log likelihood: -7380.366848
EM: Round [114] log likelihood: -7380.365476
EM: Round [115] log likelihood: -7380.364114
EM: Round [116] log likelihood: -7380.362763
EM: Round [117] log likelihood: -7380.361422
EM: Round [118] log likelihood: -7380.360091
EM: Round [119] log likelihood: -7380.358770
EM: Round [120] log likelihood: -7380.357460
EM: Round [121] log likelihood: -7380.356159
EM: Round [122] log likelihood: -7380.354869
EM: Round [123] log likelihood: -7380.353588
EM: Round [124] log likelihood: -7380.352317
EM: Round [125] log likelihood: -7380.351056
EM: Round [126] log likelihood: -7380.349804
EM: Round [127] log likelihood: -7380.348562
EM: Round [128] log likelihood: -7380.347329
EM: Round [129] log likelihood: -7380.346106
EM: Round [130] log likelihood: -7380.344892
EM: Round [131] log likelihood: -7380.343687
EM: Round [132] log likelihood: -7380.342491
EM: Round [133] log likelihood: -7380.341304
EM: Round [134] log likelihood: -7380.340126
EM: Round [135] log likelihood: -7380.338958
EM: Round [136] log likelihood: -7380.337798
EM: Round [137] log likelihood: -7380.336646
EM: Round [138] log likelihood: -7380.335504
EM: Round [139] log likelihood: -7380.334370
EM: Round [140] log likelihood: -7380.333245
EM: Round [141] log likelihood: -7380.332128
EM: Round [142] log likelihood: -7380.331019
EM: Round [143] log likelihood: -7380.329919
EM: Round [144] log likelihood: -7380.328828
EM: Round [145] log likelihood: -7380.327744
EM: Round [146] log likelihood: -7380.326668
EM: Round [147] log likelihood: -7380.325601
EM: Round [148] log likelihood: -7380.324542
EM: Round [149] log likelihood: -7380.323490
EM: Round [150] log likelihood: -7380.322447
EM: Round [151] log likelihood: -7380.321411
EM: Round [152] log likelihood: -7380.320383
EM: Round [153] log likelihood: -7380.319363
EM: Round [154] log likelihood: -7380.318351
EM: Round [155] log likelihood: -7380.317346
EM: Round [156] log likelihood: -7380.316348
EM: Round [157] log likelihood: -7380.315358
EM: Round [158] log likelihood: -7380.314376
EM: Round [159] log likelihood: -7380.313400
EM: Round [160] log likelihood: -7380.312432
EM: Round [161] log likelihood: -7380.311472
EM: Round [162] log likelihood: -7380.310518
EM: Round [163] log likelihood: -7380.309572
EM: Round [164] log likelihood: -7380.308632
EM: Round [165] log likelihood: -7380.307700
EM: Round [166] log likelihood: -7380.306774
EM: Round [167] log likelihood: -7380.305856
EM: Round [168] log likelihood: -7380.304944
EM: Round [169] log likelihood: -7380.304039
EM: Round [170] log likelihood: -7380.303141
EM: Round [171] log likelihood: -7380.302249
EM: Round [172] log likelihood: -7380.301364
EM: Round [173] log likelihood: -7380.300486
EM: Round [174] log likelihood: -7380.299614
EM: Round [175] log likelihood: -7380.298749
EM: Round [176] log likelihood: -7380.297890
EM: Round [177] log likelihood: -7380.297037
EM: Round [178] log likelihood: -7380.296191
EM: Round [179] log likelihood: -7380.295351
EM: Round [180] log likelihood: -7380.294517
EM: Round [181] log likelihood: -7380.293690
EM: Round [182] log likelihood: -7380.292868
EM: Round [183] log likelihood: -7380.292053
EM: Round [184] log likelihood: -7380.291243
EM: Round [185] log likelihood: -7380.290440
EM: Round [186] log likelihood: -7380.289642
EM: Round [187] log likelihood: -7380.288851
EM: Round [188] log likelihood: -7380.288065
EM: Round [189] log likelihood: -7380.287285
EM: Round [190] log likelihood: -7380.286511
EM: Round [191] log likelihood: -7380.285742
EM: Round [192] log likelihood: -7380.284979
EM: Round [193] log likelihood: -7380.284222
EM: Round [194] log likelihood: -7380.283471
EM: Round [195] log likelihood: -7380.282724
EM: Round [196] log likelihood: -7380.281984
EM: Round [197] log likelihood: -7380.281249
EM: Round [198] log likelihood: -7380.280519
EM: Round [199] log likelihood: -7380.279794
EM: Round [200] log likelihood: -7380.279075
EM: Round [201] log likelihood: -7380.278362
EM: Round [202] log likelihood: -7380.277653
EM: Round [203] log likelihood: -7380.276950
EM: Round [204] log likelihood: -7380.276251
EM: Round [205] log likelihood: -7380.275558
EM: Round [206] log likelihood: -7380.274870
EM: Round [207] log likelihood: -7380.274187
EM: Round [208] log likelihood: -7380.273509
EM: Round [209] log likelihood: -7380.272836
EM: Round [210] log likelihood: -7380.272168
EM: Round [211] log likelihood: -7380.271505
EM: Round [212] log likelihood: -7380.270847
EM: Round [213] log likelihood: -7380.270193
EM: Round [214] log likelihood: -7380.269544
EM: Round [215] log likelihood: -7380.268900
EM: Round [216] log likelihood: -7380.268261
EM: Round [217] log likelihood: -7380.267626
EM: Round [218] log likelihood: -7380.266996
EM: Round [219] log likelihood: -7380.266371
EM: Round [220] log likelihood: -7380.265750
EM: Round [221] log likelihood: -7380.265134
EM: Round [222] log likelihood: -7380.264522
EM: Round [223] log likelihood: -7380.263915
EM: Round [224] log likelihood: -7380.263312
EM: Round [225] log likelihood: -7380.262713
EM: Round [226] log likelihood: -7380.262119
EM: Round [227] log likelihood: -7380.261529
EM: Round [228] log likelihood: -7380.260944
EM: Round [229] log likelihood: -7380.260363
EM: Round [230] log likelihood: -7380.259785
EM: Round [231] log likelihood: -7380.259213
EM: Round [232] log likelihood: -7380.258644
EM: Round [233] log likelihood: -7380.258079
EM: Round [234] log likelihood: -7380.257519
EM: Round [235] log likelihood: -7380.256963
EM: Round [236] log likelihood: -7380.256410
EM: Round [237] log likelihood: -7380.255862
EM: Round [238] log likelihood: -7380.255318
EM: Round [239] log likelihood: -7380.254777
EM: Round [240] log likelihood: -7380.254241
EM: Round [241] log likelihood: -7380.253708
EM: Round [242] log likelihood: -7380.253179
EM: Round [243] log likelihood: -7380.252655
EM: Round [244] log likelihood: -7380.252133
EM: Round [245] log likelihood: -7380.251616
EM: Round [246] log likelihood: -7380.251103
EM: Round [247] log likelihood: -7380.250593
EM: Round [248] log likelihood: -7380.250087
EM: Round [249] log likelihood: -7380.249584
EM: Round [250] log likelihood: -7380.249085
EM: Round [251] log likelihood: -7380.248590
EM: Round [252] log likelihood: -7380.248098
EM: Round [253] log likelihood: -7380.247610
EM: Round [254] log likelihood: -7380.247126
EM: Round [255] log likelihood: -7380.246645
EM: Round [256] log likelihood: -7380.246167
EM: Round [257] log likelihood: -7380.245693
EM: Round [258] log likelihood: -7380.245222
EM: Round [259] log likelihood: -7380.244755
EM: Round [260] log likelihood: -7380.244291
EM: Round [261] log likelihood: -7380.243830
EM: Round [262] log likelihood: -7380.243373
EM: Round [263] log likelihood: -7380.242919
EM: Round [264] log likelihood: -7380.242469
EM: Round [265] log likelihood: -7380.242021
EM: Round [266] log likelihood: -7380.241577
EM: Round [267] log likelihood: -7380.241136
EM: Round [268] log likelihood: -7380.240698
EM: Round [269] log likelihood: -7380.240263
EM: Round [270] log likelihood: -7380.239832
EM: Round [271] log likelihood: -7380.239403
EM: Round [272] log likelihood: -7380.238978
EM: Round [273] log likelihood: -7380.238556
EM: Round [274] log likelihood: -7380.238137
EM: Round [275] log likelihood: -7380.237720
EM: Round [276] log likelihood: -7380.237307
EM: Round [277] log likelihood: -7380.236897
EM: Round [278] log likelihood: -7380.236489
EM: Round [279] log likelihood: -7380.236085
EM: Round [280] log likelihood: -7380.235684
EM: Round [281] log likelihood: -7380.235285
EM: Round [282] log likelihood: -7380.234889
EM: Round [283] log likelihood: -7380.234496
EM: Round [284] log likelihood: -7380.234106
EM: Round [285] log likelihood: -7380.233719
EM: Round [286] log likelihood: -7380.233335
EM: Round [287] log likelihood: -7380.232953
EM: Round [288] log likelihood: -7380.232574
EM: Round [289] log likelihood: -7380.232198
EM: Round [290] log likelihood: -7380.231824
EM: Round [291] log likelihood: -7380.231453
EM: Round [292] log likelihood: -7380.231085
EM: Round [293] log likelihood: -7380.230720
EM: Round [294] log likelihood: -7380.230357
EM: Round [295] log likelihood: -7380.229996
EM: Round [296] log likelihood: -7380.229638
EM: Round [297] log likelihood: -7380.229283
EM: Round [298] log likelihood: -7380.228931
EM: Round [299] log likelihood: -7380.228581
EM: Round [300] log likelihood: -7380.228233
EM: Round [301] log likelihood: -7380.227888
EM: Round [302] log likelihood: -7380.227545
EM: Round [303] log likelihood: -7380.227205
EM: Round [304] log likelihood: -7380.226867
EM: Round [305] log likelihood: -7380.226532
EM: Round [306] log likelihood: -7380.226199
EM: Round [307] log likelihood: -7380.225868
EM: Round [308] log likelihood: -7380.225540
EM: Round [309] log likelihood: -7380.225214
EM: Round [310] log likelihood: -7380.224891
EM: Round [311] log likelihood: -7380.224570
EM: Round [312] log likelihood: -7380.224251
EM: Round [313] log likelihood: -7380.223934
EM: Round [314] log likelihood: -7380.223620
EM: Round [315] log likelihood: -7380.223307
EM: Round [316] log likelihood: -7380.222998
EM: Round [317] log likelihood: -7380.222690
EM: Round [318] log likelihood: -7380.222384
EM: Round [319] log likelihood: -7380.222081
EM: Round [320] log likelihood: -7380.221780
EM: Round [321] log likelihood: -7380.221481
EM: Round [322] log likelihood: -7380.221184
EM: Round [323] log likelihood: -7380.220889
EM: Round [324] log likelihood: -7380.220597
EM: Round [325] log likelihood: -7380.220306
EM: Round [326] log likelihood: -7380.220018
EM: Round [327] log likelihood: -7380.219731
EM: Round [328] log likelihood: -7380.219447
EM: Round [329] log likelihood: -7380.219165
EM: Round [330] log likelihood: -7380.218884
EM: Round [331] log likelihood: -7380.218606
EM: Round [332] log likelihood: -7380.218330
EM: Round [333] log likelihood: -7380.218055
EM: Round [334] log likelihood: -7380.217783
EM: Round [335] log likelihood: -7380.217512
EM: Round [336] log likelihood: -7380.217244
EM: Round [337] log likelihood: -7380.216977
EM: Round [338] log likelihood: -7380.216712
EM: Round [339] log likelihood: -7380.216450
EM: Round [340] log likelihood: -7380.216189
EM: Round [341] log likelihood: -7380.215930
EM: Round [342] log likelihood: -7380.215672
EM: Round [343] log likelihood: -7380.215417
EM: Round [344] log likelihood: -7380.215163
EM: Round [345] log likelihood: -7380.214911
EM: Round [346] log likelihood: -7380.214661
EM: Round [347] log likelihood: -7380.214413
EM: Round [348] log likelihood: -7380.214167
EM: Round [349] log likelihood: -7380.213922
EM: Round [350] log likelihood: -7380.213679
EM: Round [351] log likelihood: -7380.213438
EM: Round [352] log likelihood: -7380.213198
EM: Round [353] log likelihood: -7380.212960
EM: Round [354] log likelihood: -7380.212724
EM: Round [355] log likelihood: -7380.212490
EM: Round [356] log likelihood: -7380.212257
EM: Round [357] log likelihood: -7380.212026
EM: Round [358] log likelihood: -7380.211796
EM: Round [359] log likelihood: -7380.211568
EM: Round [360] log likelihood: -7380.211342
EM: Round [361] log likelihood: -7380.211117
EM: Round [362] log likelihood: -7380.210894
EM: Round [363] log likelihood: -7380.210673
EM: Round [364] log likelihood: -7380.210453
EM: Round [365] log likelihood: -7380.210235
EM: Round [366] log likelihood: -7380.210018
EM: Round [367] log likelihood: -7380.209802
EM: Round [368] log likelihood: -7380.209589
EM: Round [369] log likelihood: -7380.209377
EM: Round [370] log likelihood: -7380.209166
EM: Round [371] log likelihood: -7380.208957
EM: Round [372] log likelihood: -7380.208749
EM: Round [373] log likelihood: -7380.208543
EM: Round [374] log likelihood: -7380.208338
EM: Round [375] log likelihood: -7380.208135
EM: Round [376] log likelihood: -7380.207933
EM: Round [377] log likelihood: -7380.207732
EM: Round [378] log likelihood: -7380.207533
EM: Round [379] log likelihood: -7380.207336
EM: Round [380] log likelihood: -7380.207139
EM: Round [381] log likelihood: -7380.206945
EM: Round [382] log likelihood: -7380.206751
EM: Round [383] log likelihood: -7380.206559
EM: Round [384] log likelihood: -7380.206368
EM: Round [385] log likelihood: -7380.206179
EM: Round [386] log likelihood: -7380.205991
EM: Round [387] log likelihood: -7380.205804
EM: Round [388] log likelihood: -7380.205619
EM: Round [389] log likelihood: -7380.205435
EM: Round [390] log likelihood: -7380.205252
EM: Round [391] log likelihood: -7380.205071
EM: Round [392] log likelihood: -7380.204890
EM: Round [393] log likelihood: -7380.204711
EM: Round [394] log likelihood: -7380.204534
EM: Round [395] log likelihood: -7380.204357
EM: Round [396] log likelihood: -7380.204182
EM: Round [397] log likelihood: -7380.204008
EM: Round [398] log likelihood: -7380.203836
EM: Round [399] log likelihood: -7380.203664
EM: Round [400] log likelihood: -7380.203494
EM: Round [401] log likelihood: -7380.203325
EM: Round [402] log likelihood: -7380.203157
EM: Round [403] log likelihood: -7380.202991
EM: Round [404] log likelihood: -7380.202825
EM: Round [405] log likelihood: -7380.202661
EM: Round [406] log likelihood: -7380.202498
EM: Round [407] log likelihood: -7380.202336
EM: Round [408] log likelihood: -7380.202175
EM: Round [409] log likelihood: -7380.202015
EM: Round [410] log likelihood: -7380.201857
EM: Round [411] log likelihood: -7380.201699
EM: Round [412] log likelihood: -7380.201543
EM: Round [413] log likelihood: -7380.201388
EM: Round [414] log likelihood: -7380.201234
EM: Round [415] log likelihood: -7380.201081
EM: Round [416] log likelihood: -7380.200929
EM: Round [417] log likelihood: -7380.200778
EM: Round [418] log likelihood: -7380.200628
EM: Round [419] log likelihood: -7380.200479
EM: Round [420] log likelihood: -7380.200331
EM: Round [421] log likelihood: -7380.200185
EM: Round [422] log likelihood: -7380.200039
EM: Round [423] log likelihood: -7380.199895
EM: Round [424] log likelihood: -7380.199751
EM: Round [425] log likelihood: -7380.199608
EM: Round [426] log likelihood: -7380.199467
EM: Round [427] log likelihood: -7380.199326
EM: Round [428] log likelihood: -7380.199187
EM: Round [429] log likelihood: -7380.199048
EM: Round [430] log likelihood: -7380.198911
EM: Round [431] log likelihood: -7380.198774
EM: Round [432] log likelihood: -7380.198638
EM: Round [433] log likelihood: -7380.198504
EM: Round [434] log likelihood: -7380.198370
EM: Round [435] log likelihood: -7380.198237
EM: Round [436] log likelihood: -7380.198105
EM: Round [437] log likelihood: -7380.197974
EM: Round [438] log likelihood: -7380.197844
EM: Round [439] log likelihood: -7380.197715
EM: Round [440] log likelihood: -7380.197587
EM: Round [441] log likelihood: -7380.197460
EM: Round [442] log likelihood: -7380.197333
EM: Round [443] log likelihood: -7380.197208
EM: Round [444] log likelihood: -7380.197083
EM: Round [445] log likelihood: -7380.196959
EM: Round [446] log likelihood: -7380.196837
EM: Round [447] log likelihood: -7380.196715
EM: Round [448] log likelihood: -7380.196594
EM: Round [449] log likelihood: -7380.196473
EM: Round [450] log likelihood: -7380.196354
EM: Round [451] log likelihood: -7380.196235
EM: Round [452] log likelihood: -7380.196117
EM: Round [453] log likelihood: -7380.196001
EM: Round [454] log likelihood: -7380.195884
EM: Round [455] log likelihood: -7380.195769
EM: Round [456] log likelihood: -7380.195655
EM: Round [457] log likelihood: -7380.195541
EM: Round [458] log likelihood: -7380.195428
EM: Round [459] log likelihood: -7380.195316
EM: Round [460] log likelihood: -7380.195205
EM: Round [461] log likelihood: -7380.195094
EM: Round [462] log likelihood: -7380.194985
EM: Round [463] log likelihood: -7380.194876
EM: Round [464] log likelihood: -7380.194768
EM: Round [465] log likelihood: -7380.194660
EM: Round [466] log likelihood: -7380.194554
EM: Round [467] log likelihood: -7380.194448
EM: Round [468] log likelihood: -7380.194343
EM: Round [469] log likelihood: -7380.194238
EM: Round [470] log likelihood: -7380.194134
EM: Round [471] log likelihood: -7380.194031
EM: Round [472] log likelihood: -7380.193929
EM: Round [473] log likelihood: -7380.193828
EM: Round [474] log likelihood: -7380.193727
EM: Round [475] log likelihood: -7380.193627
EM: Round [476] log likelihood: -7380.193528
EM: Stopping iterations at round 476 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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir
-done, see /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6939.091937
EM: Round [1] log likelihood: -6937.222830
EM: Round [2] log likelihood: -6937.204570
EM: Round [3] log likelihood: -6937.204430
EM: Round [4] log likelihood: -6937.204429
EM: Stopping iterations at round 4 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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295586759
Execution Time = 5.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.JjpTaMw6Cs/fi_workdir/microH.dat
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.JjpTaMw6Cs/fi_workdir/microH.dat /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/fi_workdir/microH.dat /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.JjpTaMw6Cs --json_outfile /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bjQ-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.JjpTaMw6Cs --json_outfile /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-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 [ENSG00000198237.8]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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 [ENSG00000235146.2]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000241749.4]
WARNING, no entry stored in dbm for [ENSG00000241749.4]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.JjpTaMw6Cs/ctat_genome_lib_build_dir > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.JjpTaMw6Cs/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory