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/31/b9c0404e2960a48728db7c1b06ea00/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/b9c0404e2960a48728db7c1b06ea00/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/492d969cf2e534f41f20451df9699f/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/7792d5baa09478b2edbcc355ee8e22/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/492d969cf2e534f41f20451df9699f/659_eGK-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_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-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_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/cytoBand.txt
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.HEmYH06Pph/fi_workdir --reads "/tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:41:01 ..... started STAR run
Jun 08 10:41:01 ..... loading genome
Jun 08 10:42:45 ... generating Suffix Array index
Jun 08 10:46:41 ... completed Suffix Array index
Jun 08 10:46:41 ..... processing annotations GTF
Jun 08 10:46:42 ..... inserting junctions into the genome indices
Jun 08 10:47:45 ..... started mapping
Jun 08 12:29:07 ..... finished mapping
Jun 08 12:29:09 ..... started sorting BAM
Jun 08 12:29:10 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 108.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.HEmYH06Pph/fi_workdir --reads "/tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
12:29:32 : INFO : Done.
Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3390000] -done parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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 ' => 115,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
'per_id < 96' => 11798,
'seq-similar region overlap' => 1606,
'num genes matched < 2' => 57,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'small anchor length' => 243,
' ** passed ** ' => 42912,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 111,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 505,
'excessive soft clipping' => 20078,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 68,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 48,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 102,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 30,
'low complexity anchor region' => 26
};
-writing fusion junction support info.
Execution Time = 1.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[21000] -fusion SPANNING read extraction for scaff: AC097532.3--GPR39
[1000] -fusion SPANNING read extraction for scaff: AC138035.1--SEPTIN14
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[9000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
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[565000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
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[87000] -fusion SPANNING read extraction for scaff: GUSB--NAIPP4
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[106000] -fusion SPANNING read extraction for scaff: MCM3AP--MTRNR2L12
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[192000] -fusion SPANNING read extraction for scaff: NKX2-2--NOC4L
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[65000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[70000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[74000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[73000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
[1000]
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[67000]
[68000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
[1000]
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[76000]
[77000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
[1000]
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[61000]
[62000]
[63000]
[64000]
[65000]
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[69000]
[70000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
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[78000]
[79000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
[1000]
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[3000]
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[40000]
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[42000]
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[44000]
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[49000]
[50000]
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[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4
[1000]
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[4000]
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[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9
[1000]
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[78000]
[79000]
[80000]
[81000]
[82000]
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[84000]
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[86000]
[87000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10
[1000]
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[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3
[1000]
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[15000]
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[17000]
[18000]
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[20000]
[21000]
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12
[1000]
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB7
[1000]
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[8000]
[9000]
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[11000]
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[13000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
[1000]
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[6000]
[7000]
[8000]
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[11000]
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[13000]
[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[4000]
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[6000]
[7000]
[8000]
[9000]
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[11000]
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[13000]
[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4
[1000]
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[31000]
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[33000]
[34000]
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[37000]
[38000]
[39000]
[40000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
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[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
[1000]
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[78000]
[79000]
[80000]
[81000]
[82000]
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[86000]
[87000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
[1000]
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[6000]
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[8000]
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[11000]
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[40000]
[41000]
[42000]
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[44000]
[45000]
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[50000]
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[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
[1000]
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[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
[1000]
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[3000]
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[6000]
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[11000]
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[29000]
[30000]
[31000]
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[33000]
[34000]
[35000]
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[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
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[48000]
[49000]
[50000]
[51000]
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[53000]
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[55000]
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[61000]
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[79000]
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[87000]
[88000]
[89000]
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[91000]
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[95000]
[96000]
[97000]
[98000]
[99000]
[100000]
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
[1000]
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[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA8
[1000]
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[3000]
[4000]
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[6000]
[7000]
[8000]
[9000]
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[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB6
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC5
[1000]
[2000]
[3000]
[4000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC4
[1000]
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[39000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA9
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[86000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA10
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[73000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC3
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA12
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[102000] -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB7
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[39000] -fusion SPANNING read extraction for scaff: SDHAP1--SMBD1P
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[44000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[58000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[45000] -fusion SPANNING read extraction for scaff: TAS2R14--PRR4
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[39000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[46000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[15000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[33000] -fusion SPANNING read extraction for scaff: TMEM244--ARHGAP18
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[44000] -fusion SPANNING read extraction for scaff: TRIM59--IFT80
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[12000] -fusion SPANNING read extraction for scaff: UBE2Q2P2--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 234322,
'lacks exon overlap' => 28530
};
Execution Time = 4.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -22686.086059
EM: Round [1] log likelihood: -22641.631506
EM: Round [2] log likelihood: -22633.143414
EM: Round [3] log likelihood: -22626.490431
EM: Round [4] log likelihood: -22621.165259
EM: Round [5] log likelihood: -22616.865958
EM: Round [6] log likelihood: -22613.366415
EM: Round [7] log likelihood: -22610.494775
EM: Round [8] log likelihood: -22608.119160
EM: Round [9] log likelihood: -22606.137742
EM: Round [10] log likelihood: -22604.471645
EM: Round [11] log likelihood: -22603.059691
EM: Round [12] log likelihood: -22601.854381
EM: Round [13] log likelihood: -22600.818726
EM: Round [14] log likelihood: -22599.923747
EM: Round [15] log likelihood: -22599.146517
EM: Round [16] log likelihood: -22598.468681
EM: Round [17] log likelihood: -22597.875339
EM: Round [18] log likelihood: -22597.354243
EM: Round [19] log likelihood: -22596.895208
EM: Round [20] log likelihood: -22596.489680
EM: Round [21] log likelihood: -22596.130423
EM: Round [22] log likelihood: -22595.811276
EM: Round [23] log likelihood: -22595.526972
EM: Round [24] log likelihood: -22595.272991
EM: Round [25] log likelihood: -22595.045439
EM: Round [26] log likelihood: -22594.840959
EM: Round [27] log likelihood: -22594.656648
EM: Round [28] log likelihood: -22594.489992
EM: Round [29] log likelihood: -22594.338810
EM: Round [30] log likelihood: -22594.201207
EM: Round [31] log likelihood: -22594.075537
EM: Round [32] log likelihood: -22593.960365
EM: Round [33] log likelihood: -22593.854441
EM: Round [34] log likelihood: -22593.756674
EM: Round [35] log likelihood: -22593.666111
EM: Round [36] log likelihood: -22593.581919
EM: Round [37] log likelihood: -22593.503370
EM: Round [38] log likelihood: -22593.429825
EM: Round [39] log likelihood: -22593.360725
EM: Round [40] log likelihood: -22593.295578
EM: Round [41] log likelihood: -22593.233956
EM: Round [42] log likelihood: -22593.175478
EM: Round [43] log likelihood: -22593.119813
EM: Round [44] log likelihood: -22593.066667
EM: Round [45] log likelihood: -22593.015783
EM: Round [46] log likelihood: -22592.966935
EM: Round [47] log likelihood: -22592.919921
EM: Round [48] log likelihood: -22592.874566
EM: Round [49] log likelihood: -22592.830713
EM: Round [50] log likelihood: -22592.788225
EM: Round [51] log likelihood: -22592.746980
EM: Round [52] log likelihood: -22592.706869
EM: Round [53] log likelihood: -22592.667798
EM: Round [54] log likelihood: -22592.629682
EM: Round [55] log likelihood: -22592.592445
EM: Round [56] log likelihood: -22592.556021
EM: Round [57] log likelihood: -22592.520350
EM: Round [58] log likelihood: -22592.485380
EM: Round [59] log likelihood: -22592.451063
EM: Round [60] log likelihood: -22592.417358
EM: Round [61] log likelihood: -22592.384227
EM: Round [62] log likelihood: -22592.351636
EM: Round [63] log likelihood: -22592.319555
EM: Round [64] log likelihood: -22592.287957
EM: Round [65] log likelihood: -22592.256818
EM: Round [66] log likelihood: -22592.226117
EM: Round [67] log likelihood: -22592.195832
EM: Round [68] log likelihood: -22592.165947
EM: Round [69] log likelihood: -22592.136445
EM: Round [70] log likelihood: -22592.107312
EM: Round [71] log likelihood: -22592.078535
EM: Round [72] log likelihood: -22592.050100
EM: Round [73] log likelihood: -22592.021997
EM: Round [74] log likelihood: -22591.994216
EM: Round [75] log likelihood: -22591.966748
EM: Round [76] log likelihood: -22591.939583
EM: Round [77] log likelihood: -22591.912713
EM: Round [78] log likelihood: -22591.886133
EM: Round [79] log likelihood: -22591.859833
EM: Round [80] log likelihood: -22591.833809
EM: Round [81] log likelihood: -22591.808054
EM: Round [82] log likelihood: -22591.782562
EM: Round [83] log likelihood: -22591.757328
EM: Round [84] log likelihood: -22591.732347
EM: Round [85] log likelihood: -22591.707615
EM: Round [86] log likelihood: -22591.683127
EM: Round [87] log likelihood: -22591.658878
EM: Round [88] log likelihood: -22591.634865
EM: Round [89] log likelihood: -22591.611084
EM: Round [90] log likelihood: -22591.587531
EM: Round [91] log likelihood: -22591.564203
EM: Round [92] log likelihood: -22591.541096
EM: Round [93] log likelihood: -22591.518207
EM: Round [94] log likelihood: -22591.495533
EM: Round [95] log likelihood: -22591.473071
EM: Round [96] log likelihood: -22591.450817
EM: Round [97] log likelihood: -22591.428770
EM: Round [98] log likelihood: -22591.406925
EM: Round [99] log likelihood: -22591.385281
EM: Round [100] log likelihood: -22591.363835
EM: Round [101] log likelihood: -22591.342585
EM: Round [102] log likelihood: -22591.321527
EM: Round [103] log likelihood: -22591.300660
EM: Round [104] log likelihood: -22591.279981
EM: Round [105] log likelihood: -22591.259487
EM: Round [106] log likelihood: -22591.239177
EM: Round [107] log likelihood: -22591.219049
EM: Round [108] log likelihood: -22591.199099
EM: Round [109] log likelihood: -22591.179327
EM: Round [110] log likelihood: -22591.159729
EM: Round [111] log likelihood: -22591.140305
EM: Round [112] log likelihood: -22591.121051
EM: Round [113] log likelihood: -22591.101966
EM: Round [114] log likelihood: -22591.083049
EM: Round [115] log likelihood: -22591.064296
EM: Round [116] log likelihood: -22591.045706
EM: Round [117] log likelihood: -22591.027278
EM: Round [118] log likelihood: -22591.009010
EM: Round [119] log likelihood: -22590.990899
EM: Round [120] log likelihood: -22590.972945
EM: Round [121] log likelihood: -22590.955145
EM: Round [122] log likelihood: -22590.937497
EM: Round [123] log likelihood: -22590.920001
EM: Round [124] log likelihood: -22590.902653
EM: Round [125] log likelihood: -22590.885454
EM: Round [126] log likelihood: -22590.868401
EM: Round [127] log likelihood: -22590.851492
EM: Round [128] log likelihood: -22590.834727
EM: Round [129] log likelihood: -22590.818102
EM: Round [130] log likelihood: -22590.801619
EM: Round [131] log likelihood: -22590.785273
EM: Round [132] log likelihood: -22590.769065
EM: Round [133] log likelihood: -22590.752992
EM: Round [134] log likelihood: -22590.737054
EM: Round [135] log likelihood: -22590.721248
EM: Round [136] log likelihood: -22590.705574
EM: Round [137] log likelihood: -22590.690030
EM: Round [138] log likelihood: -22590.674615
EM: Round [139] log likelihood: -22590.659328
EM: Round [140] log likelihood: -22590.644166
EM: Round [141] log likelihood: -22590.629130
EM: Round [142] log likelihood: -22590.614217
EM: Round [143] log likelihood: -22590.599427
EM: Round [144] log likelihood: -22590.584757
EM: Round [145] log likelihood: -22590.570208
EM: Round [146] log likelihood: -22590.555777
EM: Round [147] log likelihood: -22590.541464
EM: Round [148] log likelihood: -22590.527268
EM: Round [149] log likelihood: -22590.513186
EM: Round [150] log likelihood: -22590.499219
EM: Round [151] log likelihood: -22590.485364
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EM: Round [613] log likelihood: -22588.645807
EM: Round [614] log likelihood: -22588.645177
EM: Round [615] log likelihood: -22588.644551
EM: Round [616] log likelihood: -22588.643928
EM: Round [617] log likelihood: -22588.643309
EM: Round [618] log likelihood: -22588.642693
EM: Round [619] log likelihood: -22588.642081
EM: Round [620] log likelihood: -22588.641473
EM: Round [621] log likelihood: -22588.640869
EM: Round [622] log likelihood: -22588.640267
EM: Round [623] log likelihood: -22588.639670
EM: Round [624] log likelihood: -22588.639076
EM: Round [625] log likelihood: -22588.638485
EM: Round [626] log likelihood: -22588.637898
EM: Round [627] log likelihood: -22588.637314
EM: Round [628] log likelihood: -22588.636734
EM: Round [629] log likelihood: -22588.636157
EM: Round [630] log likelihood: -22588.635584
EM: Round [631] log likelihood: -22588.635014
EM: Round [632] log likelihood: -22588.634447
EM: Round [633] log likelihood: -22588.633883
EM: Round [634] log likelihood: -22588.633323
EM: Round [635] log likelihood: -22588.632766
EM: Round [636] log likelihood: -22588.632212
EM: Round [637] log likelihood: -22588.631662
EM: Round [638] log likelihood: -22588.631115
EM: Round [639] log likelihood: -22588.630571
EM: Round [640] log likelihood: -22588.630030
EM: Round [641] log likelihood: -22588.629492
EM: Round [642] log likelihood: -22588.628957
EM: Round [643] log likelihood: -22588.628426
EM: Round [644] log likelihood: -22588.627897
EM: Round [645] log likelihood: -22588.627372
EM: Round [646] log likelihood: -22588.626850
EM: Round [647] log likelihood: -22588.626331
EM: Round [648] log likelihood: -22588.625814
EM: Round [649] log likelihood: -22588.625301
EM: Round [650] log likelihood: -22588.624791
EM: Round [651] log likelihood: -22588.624284
EM: Round [652] log likelihood: -22588.623779
EM: Round [653] log likelihood: -22588.623278
EM: Round [654] log likelihood: -22588.622779
EM: Round [655] log likelihood: -22588.622284
EM: Round [656] log likelihood: -22588.621791
EM: Round [657] log likelihood: -22588.621301
EM: Round [658] log likelihood: -22588.620814
EM: Round [659] log likelihood: -22588.620330
EM: Round [660] log likelihood: -22588.619848
EM: Round [661] log likelihood: -22588.619369
EM: Round [662] log likelihood: -22588.618893
EM: Round [663] log likelihood: -22588.618420
EM: Round [664] log likelihood: -22588.617950
EM: Round [665] log likelihood: -22588.617482
EM: Round [666] log likelihood: -22588.617017
EM: Round [667] log likelihood: -22588.616554
EM: Round [668] log likelihood: -22588.616095
EM: Round [669] log likelihood: -22588.615638
EM: Round [670] log likelihood: -22588.615183
EM: Round [671] log likelihood: -22588.614731
EM: Round [672] log likelihood: -22588.614282
EM: Round [673] log likelihood: -22588.613835
EM: Round [674] log likelihood: -22588.613391
EM: Round [675] log likelihood: -22588.612950
EM: Round [676] log likelihood: -22588.612511
EM: Round [677] log likelihood: -22588.612074
EM: Round [678] log likelihood: -22588.611640
EM: Round [679] log likelihood: -22588.611209
EM: Round [680] log likelihood: -22588.610780
EM: Round [681] log likelihood: -22588.610353
EM: Round [682] log likelihood: -22588.609929
EM: Round [683] log likelihood: -22588.609507
EM: Round [684] log likelihood: -22588.609088
EM: Round [685] log likelihood: -22588.608671
EM: Round [686] log likelihood: -22588.608256
EM: Round [687] log likelihood: -22588.607844
EM: Round [688] log likelihood: -22588.607434
EM: Round [689] log likelihood: -22588.607027
EM: Round [690] log likelihood: -22588.606622
EM: Round [691] log likelihood: -22588.606219
EM: Round [692] log likelihood: -22588.605818
EM: Round [693] log likelihood: -22588.605420
EM: Round [694] log likelihood: -22588.605024
EM: Round [695] log likelihood: -22588.604630
EM: Round [696] log likelihood: -22588.604239
EM: Round [697] log likelihood: -22588.603849
EM: Round [698] log likelihood: -22588.603462
EM: Round [699] log likelihood: -22588.603077
EM: Round [700] log likelihood: -22588.602695
EM: Round [701] log likelihood: -22588.602314
EM: Round [702] log likelihood: -22588.601936
EM: Round [703] log likelihood: -22588.601559
EM: Round [704] log likelihood: -22588.601185
EM: Round [705] log likelihood: -22588.600813
EM: Round [706] log likelihood: -22588.600443
EM: Round [707] log likelihood: -22588.600076
EM: Round [708] log likelihood: -22588.599710
EM: Round [709] log likelihood: -22588.599346
EM: Round [710] log likelihood: -22588.598985
EM: Round [711] log likelihood: -22588.598625
EM: Round [712] log likelihood: -22588.598267
EM: Round [713] log likelihood: -22588.597912
EM: Round [714] log likelihood: -22588.597558
EM: Round [715] log likelihood: -22588.597207
EM: Round [716] log likelihood: -22588.596857
EM: Round [717] log likelihood: -22588.596510
EM: Round [718] log likelihood: -22588.596164
EM: Round [719] log likelihood: -22588.595820
EM: Round [720] log likelihood: -22588.595479
EM: Round [721] log likelihood: -22588.595139
EM: Round [722] log likelihood: -22588.594801
EM: Round [723] log likelihood: -22588.594465
EM: Round [724] log likelihood: -22588.594131
EM: Round [725] log likelihood: -22588.593798
EM: Round [726] log likelihood: -22588.593468
EM: Round [727] log likelihood: -22588.593139
EM: Round [728] log likelihood: -22588.592813
EM: Round [729] log likelihood: -22588.592488
EM: Round [730] log likelihood: -22588.592165
EM: Round [731] log likelihood: -22588.591843
EM: Round [732] log likelihood: -22588.591524
EM: Round [733] log likelihood: -22588.591206
EM: Round [734] log likelihood: -22588.590890
EM: Round [735] log likelihood: -22588.590576
EM: Round [736] log likelihood: -22588.590264
EM: Round [737] log likelihood: -22588.589953
EM: Round [738] log likelihood: -22588.589644
EM: Round [739] log likelihood: -22588.589337
EM: Round [740] log likelihood: -22588.589031
EM: Round [741] log likelihood: -22588.588727
EM: Round [742] log likelihood: -22588.588425
EM: Round [743] log likelihood: -22588.588125
EM: Round [744] log likelihood: -22588.587826
EM: Round [745] log likelihood: -22588.587529
EM: Round [746] log likelihood: -22588.587233
EM: Round [747] log likelihood: -22588.586939
EM: Round [748] log likelihood: -22588.586647
EM: Round [749] log likelihood: -22588.586357
EM: Round [750] log likelihood: -22588.586068
EM: Round [751] log likelihood: -22588.585780
EM: Round [752] log likelihood: -22588.585494
EM: Round [753] log likelihood: -22588.585210
EM: Round [754] log likelihood: -22588.584927
EM: Round [755] log likelihood: -22588.584646
EM: Round [756] log likelihood: -22588.584367
EM: Round [757] log likelihood: -22588.584089
EM: Round [758] log likelihood: -22588.583812
EM: Round [759] log likelihood: -22588.583537
EM: Round [760] log likelihood: -22588.583264
EM: Round [761] log likelihood: -22588.582992
EM: Round [762] log likelihood: -22588.582722
EM: Round [763] log likelihood: -22588.582453
EM: Round [764] log likelihood: -22588.582185
EM: Round [765] log likelihood: -22588.581919
EM: Round [766] log likelihood: -22588.581655
EM: Round [767] log likelihood: -22588.581391
EM: Round [768] log likelihood: -22588.581130
EM: Round [769] log likelihood: -22588.580870
EM: Round [770] log likelihood: -22588.580611
EM: Round [771] log likelihood: -22588.580353
EM: Round [772] log likelihood: -22588.580097
EM: Round [773] log likelihood: -22588.579843
EM: Round [774] log likelihood: -22588.579590
EM: Round [775] log likelihood: -22588.579338
EM: Round [776] log likelihood: -22588.579087
EM: Round [777] log likelihood: -22588.578838
EM: Round [778] log likelihood: -22588.578591
EM: Round [779] log likelihood: -22588.578344
EM: Round [780] log likelihood: -22588.578099
EM: Round [781] log likelihood: -22588.577856
EM: Round [782] log likelihood: -22588.577613
EM: Round [783] log likelihood: -22588.577372
EM: Round [784] log likelihood: -22588.577133
EM: Round [785] log likelihood: -22588.576894
EM: Round [786] log likelihood: -22588.576657
EM: Round [787] log likelihood: -22588.576421
EM: Round [788] log likelihood: -22588.576187
EM: Round [789] log likelihood: -22588.575953
EM: Round [790] log likelihood: -22588.575721
EM: Round [791] log likelihood: -22588.575491
EM: Round [792] log likelihood: -22588.575261
EM: Round [793] log likelihood: -22588.575033
EM: Round [794] log likelihood: -22588.574806
EM: Round [795] log likelihood: -22588.574580
EM: Round [796] log likelihood: -22588.574355
EM: Round [797] log likelihood: -22588.574132
EM: Round [798] log likelihood: -22588.573910
EM: Round [799] log likelihood: -22588.573689
EM: Round [800] log likelihood: -22588.573469
EM: Round [801] log likelihood: -22588.573250
EM: Round [802] log likelihood: -22588.573033
EM: Round [803] log likelihood: -22588.572817
EM: Round [804] log likelihood: -22588.572602
EM: Round [805] log likelihood: -22588.572388
EM: Round [806] log likelihood: -22588.572175
EM: Round [807] log likelihood: -22588.571963
EM: Round [808] log likelihood: -22588.571753
EM: Round [809] log likelihood: -22588.571543
EM: Round [810] log likelihood: -22588.571335
EM: Round [811] log likelihood: -22588.571128
EM: Round [812] log likelihood: -22588.570922
EM: Round [813] log likelihood: -22588.570717
EM: Round [814] log likelihood: -22588.570513
EM: Round [815] log likelihood: -22588.570310
EM: Round [816] log likelihood: -22588.570109
EM: Round [817] log likelihood: -22588.569908
EM: Round [818] log likelihood: -22588.569709
EM: Round [819] log likelihood: -22588.569510
EM: Round [820] log likelihood: -22588.569313
EM: Round [821] log likelihood: -22588.569116
EM: Round [822] log likelihood: -22588.568921
EM: Round [823] log likelihood: -22588.568727
EM: Round [824] log likelihood: -22588.568533
EM: Round [825] log likelihood: -22588.568341
EM: Round [826] log likelihood: -22588.568150
EM: Round [827] log likelihood: -22588.567960
EM: Round [828] log likelihood: -22588.567771
EM: Round [829] log likelihood: -22588.567583
EM: Round [830] log likelihood: -22588.567395
EM: Round [831] log likelihood: -22588.567209
EM: Round [832] log likelihood: -22588.567024
EM: Round [833] log likelihood: -22588.566840
EM: Round [834] log likelihood: -22588.566657
EM: Round [835] log likelihood: -22588.566474
EM: Round [836] log likelihood: -22588.566293
EM: Round [837] log likelihood: -22588.566113
EM: Round [838] log likelihood: -22588.565933
EM: Round [839] log likelihood: -22588.565755
EM: Round [840] log likelihood: -22588.565577
EM: Round [841] log likelihood: -22588.565401
EM: Round [842] log likelihood: -22588.565225
EM: Round [843] log likelihood: -22588.565050
EM: Round [844] log likelihood: -22588.564876
EM: Round [845] log likelihood: -22588.564703
EM: Round [846] log likelihood: -22588.564531
EM: Round [847] log likelihood: -22588.564360
EM: Round [848] log likelihood: -22588.564190
EM: Round [849] log likelihood: -22588.564021
EM: Round [850] log likelihood: -22588.563852
EM: Round [851] log likelihood: -22588.563685
EM: Round [852] log likelihood: -22588.563518
EM: Round [853] log likelihood: -22588.563352
EM: Round [854] log likelihood: -22588.563187
EM: Round [855] log likelihood: -22588.563023
EM: Round [856] log likelihood: -22588.562860
EM: Round [857] log likelihood: -22588.562698
EM: Round [858] log likelihood: -22588.562536
EM: Round [859] log likelihood: -22588.562375
EM: Round [860] log likelihood: -22588.562215
EM: Round [861] log likelihood: -22588.562056
EM: Round [862] log likelihood: -22588.561898
EM: Round [863] log likelihood: -22588.561741
EM: Round [864] log likelihood: -22588.561584
EM: Round [865] log likelihood: -22588.561428
EM: Round [866] log likelihood: -22588.561274
EM: Round [867] log likelihood: -22588.561119
EM: Round [868] log likelihood: -22588.560966
EM: Round [869] log likelihood: -22588.560813
EM: Round [870] log likelihood: -22588.560662
EM: Round [871] log likelihood: -22588.560511
EM: Round [872] log likelihood: -22588.560360
EM: Round [873] log likelihood: -22588.560211
EM: Round [874] log likelihood: -22588.560062
EM: Round [875] log likelihood: -22588.559914
EM: Round [876] log likelihood: -22588.559767
EM: Round [877] log likelihood: -22588.559621
EM: Round [878] log likelihood: -22588.559475
EM: Round [879] log likelihood: -22588.559330
EM: Round [880] log likelihood: -22588.559186
EM: Round [881] log likelihood: -22588.559043
EM: Round [882] log likelihood: -22588.558900
EM: Round [883] log likelihood: -22588.558758
EM: Round [884] log likelihood: -22588.558617
EM: Round [885] log likelihood: -22588.558477
EM: Round [886] log likelihood: -22588.558337
EM: Round [887] log likelihood: -22588.558198
EM: Round [888] log likelihood: -22588.558059
EM: Round [889] log likelihood: -22588.557922
EM: Round [890] log likelihood: -22588.557785
EM: Round [891] log likelihood: -22588.557648
EM: Round [892] log likelihood: -22588.557513
EM: Round [893] log likelihood: -22588.557378
EM: Round [894] log likelihood: -22588.557244
EM: Round [895] log likelihood: -22588.557110
EM: Round [896] log likelihood: -22588.556978
EM: Round [897] log likelihood: -22588.556845
EM: Round [898] log likelihood: -22588.556714
EM: Round [899] log likelihood: -22588.556583
EM: Round [900] log likelihood: -22588.556453
EM: Round [901] log likelihood: -22588.556323
EM: Round [902] log likelihood: -22588.556195
EM: Round [903] log likelihood: -22588.556066
EM: Round [904] log likelihood: -22588.555939
EM: Round [905] log likelihood: -22588.555812
EM: Round [906] log likelihood: -22588.555686
EM: Round [907] log likelihood: -22588.555560
EM: Round [908] log likelihood: -22588.555435
EM: Round [909] log likelihood: -22588.555311
EM: Round [910] log likelihood: -22588.555187
EM: Round [911] log likelihood: -22588.555064
EM: Round [912] log likelihood: -22588.554941
EM: Round [913] log likelihood: -22588.554819
EM: Round [914] log likelihood: -22588.554698
EM: Round [915] log likelihood: -22588.554578
EM: Round [916] log likelihood: -22588.554457
EM: Round [917] log likelihood: -22588.554338
EM: Round [918] log likelihood: -22588.554219
EM: Round [919] log likelihood: -22588.554101
EM: Round [920] log likelihood: -22588.553983
EM: Round [921] log likelihood: -22588.553866
EM: Round [922] log likelihood: -22588.553750
EM: Round [923] log likelihood: -22588.553634
EM: Round [924] log likelihood: -22588.553518
EM: Round [925] log likelihood: -22588.553403
EM: Round [926] log likelihood: -22588.553289
EM: Round [927] log likelihood: -22588.553176
EM: Round [928] log likelihood: -22588.553062
EM: Round [929] log likelihood: -22588.552950
EM: Round [930] log likelihood: -22588.552838
EM: Round [931] log likelihood: -22588.552727
EM: Round [932] log likelihood: -22588.552616
EM: Round [933] log likelihood: -22588.552505
EM: Round [934] log likelihood: -22588.552396
EM: Round [935] log likelihood: -22588.552286
EM: Round [936] log likelihood: -22588.552178
EM: Round [937] log likelihood: -22588.552070
EM: Round [938] log likelihood: -22588.551962
EM: Round [939] log likelihood: -22588.551855
EM: Round [940] log likelihood: -22588.551748
EM: Round [941] log likelihood: -22588.551642
EM: Round [942] log likelihood: -22588.551537
EM: Round [943] log likelihood: -22588.551432
EM: Round [944] log likelihood: -22588.551327
EM: Round [945] log likelihood: -22588.551223
EM: Round [946] log likelihood: -22588.551120
EM: Round [947] log likelihood: -22588.551017
EM: Round [948] log likelihood: -22588.550914
EM: Round [949] log likelihood: -22588.550812
EM: Round [950] log likelihood: -22588.550711
EM: Round [951] log likelihood: -22588.550610
EM: Round [952] log likelihood: -22588.550509
EM: Round [953] log likelihood: -22588.550409
EM: Stopping iterations at round 953 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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir
-done, see /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -16195.754994
EM: Round [1] log likelihood: -16191.619086
EM: Round [2] log likelihood: -16191.592622
EM: Round [3] log likelihood: -16191.592107
EM: Round [4] log likelihood: -16191.592094
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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295934893
Execution Time = 5.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/fi_workdir/microH.dat
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.HEmYH06Pph/fi_workdir/microH.dat /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/fi_workdir/microH.dat /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HEmYH06Pph --json_outfile /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eGK-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.HEmYH06Pph --json_outfile /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000259429.5]
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 [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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000251634.2]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000283426.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory