Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/c42e82f10399702d7bf5cacc08e26a/659_Fr-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/2e7d9846e123f7c46ef5e3474b0162/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/343f663539b695113a2456e280402c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/343f663539b695113a2456e280402c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/c42e82f10399702d7bf5cacc08e26a/659_Fr-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_Fr-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/cytoBand.txt
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_Fr-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.EVTZxZ8xgB/fi_workdir --reads "/tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:59:03 ..... started STAR run
Jun 08 09:59:03 ..... loading genome
Jun 08 10:00:44 ... generating Suffix Array index
Jun 08 10:04:23 ... completed Suffix Array index
Jun 08 10:04:23 ..... processing annotations GTF
Jun 08 10:04:24 ..... inserting junctions into the genome indices
Jun 08 10:05:24 ..... started mapping
Jun 08 11:05:26 ..... finished mapping
Jun 08 11:05:27 ..... started sorting BAM
Jun 08 11:05:29 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 66.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_Fr-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.EVTZxZ8xgB/fi_workdir --reads "/tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:05:53 : INFO : Done.
Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3830000] -done parsing /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 659,
'low complexity anchor region' => 30,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
'excessive soft clipping' => 23762,
' ** passed ** ' => 29858,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 197,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 78,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 334,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 50,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'small anchor length' => 264,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 69,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 52,
'exons hit < 2' => 6,
'per_id < 96' => 13788,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 96,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 33,
'seq-similar region overlap' => 341,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 3
};
-writing fusion junction support info.
Execution Time = 2.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[29000] -fusion SPANNING read extraction for scaff: AC004918.3--ULK4
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[20000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[162000] -fusion SPANNING read extraction for scaff: ACP3--ETV1
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[300000] -fusion SPANNING read extraction for scaff: AL611929.1--AFDN
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[149000] -fusion SPANNING read extraction for scaff: ATF6--SORL1
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[24000] -fusion SPANNING read extraction for scaff: ATF6--AP002365.1
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[28000] -fusion SPANNING read extraction for scaff: ATF6--AP000977.1
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[27000] -fusion SPANNING read extraction for scaff: ATG7--PPM1D
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[32000] -fusion SPANNING read extraction for scaff: COP1--PRDX6-AS1
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[97000] -fusion SPANNING read extraction for scaff: DCAF1--SEC61A1
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[60000] -fusion SPANNING read extraction for scaff: DENND11--ULK4
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[26000] -fusion SPANNING read extraction for scaff: ELL2--PCBP2P3
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[26000] -fusion SPANNING read extraction for scaff: ELL2--AC114316.1
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[17000] -fusion SPANNING read extraction for scaff: ENTPD7--EYA1
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[23000] -fusion SPANNING read extraction for scaff: ERO1A--TXNDC16
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[303000] -fusion SPANNING read extraction for scaff: FRMD1--AFDN
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[209000] -fusion SPANNING read extraction for scaff: GALNT17--AUTS2
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[160000] -fusion SPANNING read extraction for scaff: IRS2--CYFIP1
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[37000] -fusion SPANNING read extraction for scaff: JMJD6--ERN1
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[67000] -fusion SPANNING read extraction for scaff: KIAA1671--AC007731.2
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[67000] -fusion SPANNING read extraction for scaff: KIAA1671--FAM230J
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[165000] -fusion SPANNING read extraction for scaff: LAMA3--OSBPL1A
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[22000] -fusion SPANNING read extraction for scaff: MAP2K4--JMJD6
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[63000] -fusion SPANNING read extraction for scaff: MCF2L--AP006261.1
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[18000] -fusion SPANNING read extraction for scaff: MSI2--AC092674.1
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[18000] -fusion SPANNING read extraction for scaff: MSI2--CXCL13
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[21000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[19000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[20000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[18000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[16000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[18000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[41000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[30000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[41000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[41000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[40000] -fusion SPANNING read extraction for scaff: PRDX6-AS1--RABGAP1L
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[331000] -fusion SPANNING read extraction for scaff: SEC61A1--CHD3
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[63000] -fusion SPANNING read extraction for scaff: SOS2--TAMM41
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[21000] -fusion SPANNING read extraction for scaff: TGS1--AC138035.1
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[32000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[33000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[37000] -fusion SPANNING read extraction for scaff: TMC5--AC002331.1
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[37000] -fusion SPANNING read extraction for scaff: TMC5--AC009035.1
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[66000] -fusion SPANNING read extraction for scaff: TTC28--CHEK2
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[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[9000] -fusion SPANNING read extraction for scaff: UPK3B--AC211476.4
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[31000] -fusion SPANNING read extraction for scaff: ZCCHC7--BX255923.2
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[10000] -fusion SPANNING read extraction for scaff: ZNF431--FGF13
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 34093,
'seq similar region alignment' => 106529
};
Execution Time = 5.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -16174.940451
EM: Round [1] log likelihood: -16167.607929
EM: Round [2] log likelihood: -16164.831111
EM: Round [3] log likelihood: -16162.602757
EM: Round [4] log likelihood: -16160.789316
EM: Round [5] log likelihood: -16159.295804
EM: Round [6] log likelihood: -16158.052304
EM: Round [7] log likelihood: -16157.006556
EM: Round [8] log likelihood: -16156.118970
EM: Round [9] log likelihood: -16155.359185
EM: Round [10] log likelihood: -16154.703655
EM: Round [11] log likelihood: -16154.133920
EM: Round [12] log likelihood: -16153.635362
EM: Round [13] log likelihood: -16153.196294
EM: Round [14] log likelihood: -16152.807288
EM: Round [15] log likelihood: -16152.460669
EM: Round [16] log likelihood: -16152.150145
EM: Round [17] log likelihood: -16151.870514
EM: Round [18] log likelihood: -16151.617449
EM: Round [19] log likelihood: -16151.387325
EM: Round [20] log likelihood: -16151.177094
EM: Round [21] log likelihood: -16150.984172
EM: Round [22] log likelihood: -16150.806366
EM: Round [23] log likelihood: -16150.641802
EM: Round [24] log likelihood: -16150.488874
EM: Round [25] log likelihood: -16150.346203
EM: Round [26] log likelihood: -16150.212599
EM: Round [27] log likelihood: -16150.087033
EM: Round [28] log likelihood: -16149.968614
EM: Round [29] log likelihood: -16149.856568
EM: Round [30] log likelihood: -16149.750220
EM: Round [31] log likelihood: -16149.648984
EM: Round [32] log likelihood: -16149.552346
EM: Round [33] log likelihood: -16149.459856
EM: Round [34] log likelihood: -16149.371120
EM: Round [35] log likelihood: -16149.285793
EM: Round [36] log likelihood: -16149.203569
EM: Round [37] log likelihood: -16149.124182
EM: Round [38] log likelihood: -16149.047393
EM: Round [39] log likelihood: -16148.972993
EM: Round [40] log likelihood: -16148.900797
EM: Round [41] log likelihood: -16148.830640
EM: Round [42] log likelihood: -16148.762376
EM: Round [43] log likelihood: -16148.695874
EM: Round [44] log likelihood: -16148.631017
EM: Round [45] log likelihood: -16148.567702
EM: Round [46] log likelihood: -16148.505834
EM: Round [47] log likelihood: -16148.445330
EM: Round [48] log likelihood: -16148.386114
EM: Round [49] log likelihood: -16148.328117
EM: Round [50] log likelihood: -16148.271279
EM: Round [51] log likelihood: -16148.215541
EM: Round [52] log likelihood: -16148.160855
EM: Round [53] log likelihood: -16148.107171
EM: Round [54] log likelihood: -16148.054449
EM: Round [55] log likelihood: -16148.002648
EM: Round [56] log likelihood: -16147.951734
EM: Round [57] log likelihood: -16147.901672
EM: Round [58] log likelihood: -16147.852431
EM: Round [59] log likelihood: -16147.803984
EM: Round [60] log likelihood: -16147.756304
EM: Round [61] log likelihood: -16147.709366
EM: Round [62] log likelihood: -16147.663146
EM: Round [63] log likelihood: -16147.617625
EM: Round [64] log likelihood: -16147.572780
EM: Round [65] log likelihood: -16147.528593
EM: Round [66] log likelihood: -16147.485046
EM: Round [67] log likelihood: -16147.442122
EM: Round [68] log likelihood: -16147.399805
EM: Round [69] log likelihood: -16147.358079
EM: Round [70] log likelihood: -16147.316930
EM: Round [71] log likelihood: -16147.276343
EM: Round [72] log likelihood: -16147.236306
EM: Round [73] log likelihood: -16147.196806
EM: Round [74] log likelihood: -16147.157831
EM: Round [75] log likelihood: -16147.119368
EM: Round [76] log likelihood: -16147.081408
EM: Round [77] log likelihood: -16147.043938
EM: Round [78] log likelihood: -16147.006950
EM: Round [79] log likelihood: -16146.970432
EM: Round [80] log likelihood: -16146.934375
EM: Round [81] log likelihood: -16146.898770
EM: Round [82] log likelihood: -16146.863608
EM: Round [83] log likelihood: -16146.828881
EM: Round [84] log likelihood: -16146.794579
EM: Round [85] log likelihood: -16146.760694
EM: Round [86] log likelihood: -16146.727220
EM: Round [87] log likelihood: -16146.694148
EM: Round [88] log likelihood: -16146.661470
EM: Round [89] log likelihood: -16146.629180
EM: Round [90] log likelihood: -16146.597271
EM: Round [91] log likelihood: -16146.565735
EM: Round [92] log likelihood: -16146.534566
EM: Round [93] log likelihood: -16146.503758
EM: Round [94] log likelihood: -16146.473304
EM: Round [95] log likelihood: -16146.443198
EM: Round [96] log likelihood: -16146.413435
EM: Round [97] log likelihood: -16146.384008
EM: Round [98] log likelihood: -16146.354912
EM: Round [99] log likelihood: -16146.326141
EM: Round [100] log likelihood: -16146.297690
EM: Round [101] log likelihood: -16146.269554
EM: Round [102] log likelihood: -16146.241727
EM: Round [103] log likelihood: -16146.214205
EM: Round [104] log likelihood: -16146.186983
EM: Round [105] log likelihood: -16146.160055
EM: Round [106] log likelihood: -16146.133418
EM: Round [107] log likelihood: -16146.107066
EM: Round [108] log likelihood: -16146.080996
EM: Round [109] log likelihood: -16146.055202
EM: Round [110] log likelihood: -16146.029681
EM: Round [111] log likelihood: -16146.004429
EM: Round [112] log likelihood: -16145.979441
EM: Round [113] log likelihood: -16145.954713
EM: Round [114] log likelihood: -16145.930241
EM: Round [115] log likelihood: -16145.906023
EM: Round [116] log likelihood: -16145.882053
EM: Round [117] log likelihood: -16145.858328
EM: Round [118] log likelihood: -16145.834845
EM: Round [119] log likelihood: -16145.811601
EM: Round [120] log likelihood: -16145.788590
EM: Round [121] log likelihood: -16145.765812
EM: Round [122] log likelihood: -16145.743261
EM: Round [123] log likelihood: -16145.720935
EM: Round [124] log likelihood: -16145.698831
EM: Round [125] log likelihood: -16145.676945
EM: Round [126] log likelihood: -16145.655274
EM: Round [127] log likelihood: -16145.633816
EM: Round [128] log likelihood: -16145.612568
EM: Round [129] log likelihood: -16145.591526
EM: Round [130] log likelihood: -16145.570688
EM: Round [131] log likelihood: -16145.550051
EM: Round [132] log likelihood: -16145.529613
EM: Round [133] log likelihood: -16145.509370
EM: Round [134] log likelihood: -16145.489320
EM: Round [135] log likelihood: -16145.469460
EM: Round [136] log likelihood: -16145.449789
EM: Round [137] log likelihood: -16145.430303
EM: Round [138] log likelihood: -16145.411000
EM: Round [139] log likelihood: -16145.391878
EM: Round [140] log likelihood: -16145.372934
EM: Round [141] log likelihood: -16145.354166
EM: Round [142] log likelihood: -16145.335572
EM: Round [143] log likelihood: -16145.317150
EM: Round [144] log likelihood: -16145.298896
EM: Round [145] log likelihood: -16145.280810
EM: Round [146] log likelihood: -16145.262889
EM: Round [147] log likelihood: -16145.245131
EM: Round [148] log likelihood: -16145.227535
EM: Round [149] log likelihood: -16145.210097
EM: Round [150] log likelihood: -16145.192816
EM: Round [151] log likelihood: -16145.175690
EM: Round [152] log likelihood: -16145.158717
EM: Round [153] log likelihood: -16145.141896
EM: Round [154] log likelihood: -16145.125224
EM: Round [155] log likelihood: -16145.108699
EM: Round [156] log likelihood: -16145.092321
EM: Round [157] log likelihood: -16145.076087
EM: Round [158] log likelihood: -16145.059995
EM: Round [159] log likelihood: -16145.044044
EM: Round [160] log likelihood: -16145.028231
EM: Round [161] log likelihood: -16145.012556
EM: Round [162] log likelihood: -16144.997017
EM: Round [163] log likelihood: -16144.981613
EM: Round [164] log likelihood: -16144.966340
EM: Round [165] log likelihood: -16144.951199
EM: Round [166] log likelihood: -16144.936187
EM: Round [167] log likelihood: -16144.921304
EM: Round [168] log likelihood: -16144.906547
EM: Round [169] log likelihood: -16144.891915
EM: Round [170] log likelihood: -16144.877407
EM: Round [171] log likelihood: -16144.863021
EM: Round [172] log likelihood: -16144.848756
EM: Round [173] log likelihood: -16144.834611
EM: Round [174] log likelihood: -16144.820584
EM: Round [175] log likelihood: -16144.806673
EM: Round [176] log likelihood: -16144.792879
EM: Round [177] log likelihood: -16144.779199
EM: Round [178] log likelihood: -16144.765631
EM: Round [179] log likelihood: -16144.752176
EM: Round [180] log likelihood: -16144.738831
EM: Round [181] log likelihood: -16144.725595
EM: Round [182] log likelihood: -16144.712468
EM: Round [183] log likelihood: -16144.699448
EM: Round [184] log likelihood: -16144.686533
EM: Round [185] log likelihood: -16144.673724
EM: Round [186] log likelihood: -16144.661017
EM: Round [187] log likelihood: -16144.648414
EM: Round [188] log likelihood: -16144.635911
EM: Round [189] log likelihood: -16144.623509
EM: Round [190] log likelihood: -16144.611206
EM: Round [191] log likelihood: -16144.599002
EM: Round [192] log likelihood: -16144.586894
EM: Round [193] log likelihood: -16144.574883
EM: Round [194] log likelihood: -16144.562966
EM: Round [195] log likelihood: -16144.551144
EM: Round [196] log likelihood: -16144.539415
EM: Round [197] log likelihood: -16144.527778
EM: Round [198] log likelihood: -16144.516233
EM: Round [199] log likelihood: -16144.504777
EM: Round [200] log likelihood: -16144.493411
EM: Round [201] log likelihood: -16144.482134
EM: Round [202] log likelihood: -16144.470944
EM: Round [203] log likelihood: -16144.459841
EM: Round [204] log likelihood: -16144.448823
EM: Round [205] log likelihood: -16144.437891
EM: Round [206] log likelihood: -16144.427042
EM: Round [207] log likelihood: -16144.416277
EM: Round [208] log likelihood: -16144.405594
EM: Round [209] log likelihood: -16144.394992
EM: Round [210] log likelihood: -16144.384471
EM: Round [211] log likelihood: -16144.374031
EM: Round [212] log likelihood: -16144.363669
EM: Round [213] log likelihood: -16144.353386
EM: Round [214] log likelihood: -16144.343180
EM: Round [215] log likelihood: -16144.333051
EM: Round [216] log likelihood: -16144.322999
EM: Round [217] log likelihood: -16144.313021
EM: Round [218] log likelihood: -16144.303118
EM: Round [219] log likelihood: -16144.293289
EM: Round [220] log likelihood: -16144.283534
EM: Round [221] log likelihood: -16144.273850
EM: Round [222] log likelihood: -16144.264239
EM: Round [223] log likelihood: -16144.254698
EM: Round [224] log likelihood: -16144.245228
EM: Round [225] log likelihood: -16144.235828
EM: Round [226] log likelihood: -16144.226496
EM: Round [227] log likelihood: -16144.217233
EM: Round [228] log likelihood: -16144.208038
EM: Round [229] log likelihood: -16144.198910
EM: Round [230] log likelihood: -16144.189848
EM: Round [231] log likelihood: -16144.180852
EM: Round [232] log likelihood: -16144.171922
EM: Round [233] log likelihood: -16144.163056
EM: Round [234] log likelihood: -16144.154254
EM: Round [235] log likelihood: -16144.145515
EM: Round [236] log likelihood: -16144.136840
EM: Round [237] log likelihood: -16144.128226
EM: Round [238] log likelihood: -16144.119674
EM: Round [239] log likelihood: -16144.111184
EM: Round [240] log likelihood: -16144.102754
EM: Round [241] log likelihood: -16144.094383
EM: Round [242] log likelihood: -16144.086073
EM: Round [243] log likelihood: -16144.077821
EM: Round [244] log likelihood: -16144.069628
EM: Round [245] log likelihood: -16144.061492
EM: Round [246] log likelihood: -16144.053414
EM: Round [247] log likelihood: -16144.045392
EM: Round [248] log likelihood: -16144.037427
EM: Round [249] log likelihood: -16144.029517
EM: Round [250] log likelihood: -16144.021663
EM: Round [251] log likelihood: -16144.013864
EM: Round [252] log likelihood: -16144.006119
EM: Round [253] log likelihood: -16143.998427
EM: Round [254] log likelihood: -16143.990789
EM: Round [255] log likelihood: -16143.983204
EM: Round [256] log likelihood: -16143.975671
EM: Round [257] log likelihood: -16143.968190
EM: Round [258] log likelihood: -16143.960761
EM: Round [259] log likelihood: -16143.953383
EM: Round [260] log likelihood: -16143.946055
EM: Round [261] log likelihood: -16143.938777
EM: Round [262] log likelihood: -16143.931549
EM: Round [263] log likelihood: -16143.924370
EM: Round [264] log likelihood: -16143.917240
EM: Round [265] log likelihood: -16143.910159
EM: Round [266] log likelihood: -16143.903125
EM: Round [267] log likelihood: -16143.896139
EM: Round [268] log likelihood: -16143.889200
EM: Round [269] log likelihood: -16143.882308
EM: Round [270] log likelihood: -16143.875462
EM: Round [271] log likelihood: -16143.868662
EM: Round [272] log likelihood: -16143.861908
EM: Round [273] log likelihood: -16143.855199
EM: Round [274] log likelihood: -16143.848534
EM: Round [275] log likelihood: -16143.841914
EM: Round [276] log likelihood: -16143.835338
EM: Round [277] log likelihood: -16143.828806
EM: Round [278] log likelihood: -16143.822317
EM: Round [279] log likelihood: -16143.815871
EM: Round [280] log likelihood: -16143.809467
EM: Round [281] log likelihood: -16143.803106
EM: Round [282] log likelihood: -16143.796786
EM: Round [283] log likelihood: -16143.790508
EM: Round [284] log likelihood: -16143.784271
EM: Round [285] log likelihood: -16143.778075
EM: Round [286] log likelihood: -16143.771919
EM: Round [287] log likelihood: -16143.765804
EM: Round [288] log likelihood: -16143.759728
EM: Round [289] log likelihood: -16143.753692
EM: Round [290] log likelihood: -16143.747695
EM: Round [291] log likelihood: -16143.741736
EM: Round [292] log likelihood: -16143.735816
EM: Round [293] log likelihood: -16143.729935
EM: Round [294] log likelihood: -16143.724091
EM: Round [295] log likelihood: -16143.718285
EM: Round [296] log likelihood: -16143.712516
EM: Round [297] log likelihood: -16143.706784
EM: Round [298] log likelihood: -16143.701088
EM: Round [299] log likelihood: -16143.695429
EM: Round [300] log likelihood: -16143.689806
EM: Round [301] log likelihood: -16143.684219
EM: Round [302] log likelihood: -16143.678667
EM: Round [303] log likelihood: -16143.673151
EM: Round [304] log likelihood: -16143.667669
EM: Round [305] log likelihood: -16143.662222
EM: Round [306] log likelihood: -16143.656810
EM: Round [307] log likelihood: -16143.651431
EM: Round [308] log likelihood: -16143.646086
EM: Round [309] log likelihood: -16143.640775
EM: Round [310] log likelihood: -16143.635497
EM: Round [311] log likelihood: -16143.630252
EM: Round [312] log likelihood: -16143.625040
EM: Round [313] log likelihood: -16143.619860
EM: Round [314] log likelihood: -16143.614712
EM: Round [315] log likelihood: -16143.609597
EM: Round [316] log likelihood: -16143.604513
EM: Round [317] log likelihood: -16143.599461
EM: Round [318] log likelihood: -16143.594439
EM: Round [319] log likelihood: -16143.589449
EM: Round [320] log likelihood: -16143.584490
EM: Round [321] log likelihood: -16143.579561
EM: Round [322] log likelihood: -16143.574662
EM: Round [323] log likelihood: -16143.569793
EM: Round [324] log likelihood: -16143.564954
EM: Round [325] log likelihood: -16143.560145
EM: Round [326] log likelihood: -16143.555365
EM: Round [327] log likelihood: -16143.550614
EM: Round [328] log likelihood: -16143.545892
EM: Round [329] log likelihood: -16143.541199
EM: Round [330] log likelihood: -16143.536534
EM: Round [331] log likelihood: -16143.531897
EM: Round [332] log likelihood: -16143.527288
EM: Round [333] log likelihood: -16143.522707
EM: Round [334] log likelihood: -16143.518154
EM: Round [335] log likelihood: -16143.513628
EM: Round [336] log likelihood: -16143.509129
EM: Round [337] log likelihood: -16143.504657
EM: Round [338] log likelihood: -16143.500212
EM: Round [339] log likelihood: -16143.495793
EM: Round [340] log likelihood: -16143.491401
EM: Round [341] log likelihood: -16143.487034
EM: Round [342] log likelihood: -16143.482694
EM: Round [343] log likelihood: -16143.478380
EM: Round [344] log likelihood: -16143.474091
EM: Round [345] log likelihood: -16143.469827
EM: Round [346] log likelihood: -16143.465589
EM: Round [347] log likelihood: -16143.461375
EM: Round [348] log likelihood: -16143.457187
EM: Round [349] log likelihood: -16143.453022
EM: Round [350] log likelihood: -16143.448883
EM: Round [351] log likelihood: -16143.444767
EM: Round [352] log likelihood: -16143.440676
EM: Round [353] log likelihood: -16143.436609
EM: Round [354] log likelihood: -16143.432565
EM: Round [355] log likelihood: -16143.428545
EM: Round [356] log likelihood: -16143.424548
EM: Round [357] log likelihood: -16143.420574
EM: Round [358] log likelihood: -16143.416624
EM: Round [359] log likelihood: -16143.412696
EM: Round [360] log likelihood: -16143.408791
EM: Round [361] log likelihood: -16143.404908
EM: Round [362] log likelihood: -16143.401048
EM: Round [363] log likelihood: -16143.397210
EM: Round [364] log likelihood: -16143.393394
EM: Round [365] log likelihood: -16143.389600
EM: Round [366] log likelihood: -16143.385827
EM: Round [367] log likelihood: -16143.382076
EM: Round [368] log likelihood: -16143.378347
EM: Round [369] log likelihood: -16143.374638
EM: Round [370] log likelihood: -16143.370951
EM: Round [371] log likelihood: -16143.367285
EM: Round [372] log likelihood: -16143.363639
EM: Round [373] log likelihood: -16143.360015
EM: Round [374] log likelihood: -16143.356410
EM: Round [375] log likelihood: -16143.352826
EM: Round [376] log likelihood: -16143.349262
EM: Round [377] log likelihood: -16143.345718
EM: Round [378] log likelihood: -16143.342194
EM: Round [379] log likelihood: -16143.338690
EM: Round [380] log likelihood: -16143.335206
EM: Round [381] log likelihood: -16143.331740
EM: Round [382] log likelihood: -16143.328295
EM: Round [383] log likelihood: -16143.324868
EM: Round [384] log likelihood: -16143.321461
EM: Round [385] log likelihood: -16143.318072
EM: Round [386] log likelihood: -16143.314702
EM: Round [387] log likelihood: -16143.311351
EM: Round [388] log likelihood: -16143.308018
EM: Round [389] log likelihood: -16143.304704
EM: Round [390] log likelihood: -16143.301408
EM: Round [391] log likelihood: -16143.298130
EM: Round [392] log likelihood: -16143.294871
EM: Round [393] log likelihood: -16143.291629
EM: Round [394] log likelihood: -16143.288405
EM: Round [395] log likelihood: -16143.285198
EM: Round [396] log likelihood: -16143.282009
EM: Round [397] log likelihood: -16143.278838
EM: Round [398] log likelihood: -16143.275683
EM: Round [399] log likelihood: -16143.272546
EM: Round [400] log likelihood: -16143.269426
EM: Round [401] log likelihood: -16143.266323
EM: Round [402] log likelihood: -16143.263237
EM: Round [403] log likelihood: -16143.260167
EM: Round [404] log likelihood: -16143.257114
EM: Round [405] log likelihood: -16143.254077
EM: Round [406] log likelihood: -16143.251057
EM: Round [407] log likelihood: -16143.248052
EM: Round [408] log likelihood: -16143.245064
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EM: Round [865] log likelihood: -16142.672450
EM: Round [866] log likelihood: -16142.671980
EM: Round [867] log likelihood: -16142.671511
EM: Round [868] log likelihood: -16142.671043
EM: Round [869] log likelihood: -16142.670576
EM: Round [870] log likelihood: -16142.670112
EM: Round [871] log likelihood: -16142.669648
EM: Round [872] log likelihood: -16142.669186
EM: Round [873] log likelihood: -16142.668726
EM: Round [874] log likelihood: -16142.668267
EM: Round [875] log likelihood: -16142.667809
EM: Round [876] log likelihood: -16142.667353
EM: Round [877] log likelihood: -16142.666898
EM: Round [878] log likelihood: -16142.666444
EM: Round [879] log likelihood: -16142.665992
EM: Round [880] log likelihood: -16142.665541
EM: Round [881] log likelihood: -16142.665092
EM: Round [882] log likelihood: -16142.664644
EM: Round [883] log likelihood: -16142.664198
EM: Round [884] log likelihood: -16142.663752
EM: Round [885] log likelihood: -16142.663309
EM: Round [886] log likelihood: -16142.662866
EM: Round [887] log likelihood: -16142.662425
EM: Round [888] log likelihood: -16142.661985
EM: Round [889] log likelihood: -16142.661547
EM: Round [890] log likelihood: -16142.661110
EM: Round [891] log likelihood: -16142.660674
EM: Round [892] log likelihood: -16142.660240
EM: Round [893] log likelihood: -16142.659807
EM: Round [894] log likelihood: -16142.659375
EM: Round [895] log likelihood: -16142.658944
EM: Round [896] log likelihood: -16142.658515
EM: Round [897] log likelihood: -16142.658087
EM: Round [898] log likelihood: -16142.657661
EM: Round [899] log likelihood: -16142.657236
EM: Round [900] log likelihood: -16142.656812
EM: Round [901] log likelihood: -16142.656389
EM: Round [902] log likelihood: -16142.655968
EM: Round [903] log likelihood: -16142.655547
EM: Round [904] log likelihood: -16142.655129
EM: Round [905] log likelihood: -16142.654711
EM: Round [906] log likelihood: -16142.654295
EM: Round [907] log likelihood: -16142.653880
EM: Round [908] log likelihood: -16142.653466
EM: Round [909] log likelihood: -16142.653053
EM: Round [910] log likelihood: -16142.652642
EM: Round [911] log likelihood: -16142.652232
EM: Round [912] log likelihood: -16142.651823
EM: Round [913] log likelihood: -16142.651415
EM: Round [914] log likelihood: -16142.651009
EM: Round [915] log likelihood: -16142.650604
EM: Round [916] log likelihood: -16142.650200
EM: Round [917] log likelihood: -16142.649797
EM: Round [918] log likelihood: -16142.649395
EM: Round [919] log likelihood: -16142.648995
EM: Round [920] log likelihood: -16142.648596
EM: Round [921] log likelihood: -16142.648198
EM: Round [922] log likelihood: -16142.647801
EM: Round [923] log likelihood: -16142.647405
EM: Round [924] log likelihood: -16142.647011
EM: Round [925] log likelihood: -16142.646618
EM: Round [926] log likelihood: -16142.646226
EM: Round [927] log likelihood: -16142.645835
EM: Round [928] log likelihood: -16142.645445
EM: Round [929] log likelihood: -16142.645056
EM: Round [930] log likelihood: -16142.644669
EM: Round [931] log likelihood: -16142.644283
EM: Round [932] log likelihood: -16142.643897
EM: Round [933] log likelihood: -16142.643513
EM: Round [934] log likelihood: -16142.643130
EM: Round [935] log likelihood: -16142.642749
EM: Round [936] log likelihood: -16142.642368
EM: Round [937] log likelihood: -16142.641989
EM: Round [938] log likelihood: -16142.641610
EM: Round [939] log likelihood: -16142.641233
EM: Round [940] log likelihood: -16142.640857
EM: Round [941] log likelihood: -16142.640482
EM: Round [942] log likelihood: -16142.640108
EM: Round [943] log likelihood: -16142.639735
EM: Round [944] log likelihood: -16142.639363
EM: Round [945] log likelihood: -16142.638992
EM: Round [946] log likelihood: -16142.638623
EM: Round [947] log likelihood: -16142.638254
EM: Round [948] log likelihood: -16142.637887
EM: Round [949] log likelihood: -16142.637521
EM: Round [950] log likelihood: -16142.637155
EM: Round [951] log likelihood: -16142.636791
EM: Round [952] log likelihood: -16142.636428
EM: Round [953] log likelihood: -16142.636066
EM: Round [954] log likelihood: -16142.635705
EM: Round [955] log likelihood: -16142.635345
EM: Round [956] log likelihood: -16142.634986
EM: Round [957] log likelihood: -16142.634628
EM: Round [958] log likelihood: -16142.634271
EM: Round [959] log likelihood: -16142.633916
EM: Round [960] log likelihood: -16142.633561
EM: Round [961] log likelihood: -16142.633207
EM: Round [962] log likelihood: -16142.632854
EM: Round [963] log likelihood: -16142.632503
EM: Round [964] log likelihood: -16142.632152
EM: Round [965] log likelihood: -16142.631802
EM: Round [966] log likelihood: -16142.631454
EM: Round [967] log likelihood: -16142.631106
EM: Round [968] log likelihood: -16142.630759
EM: Round [969] log likelihood: -16142.630414
EM: Round [970] log likelihood: -16142.630069
EM: Round [971] log likelihood: -16142.629726
EM: Round [972] log likelihood: -16142.629383
EM: Round [973] log likelihood: -16142.629041
EM: Round [974] log likelihood: -16142.628701
EM: Round [975] log likelihood: -16142.628361
EM: Round [976] log likelihood: -16142.628022
EM: Round [977] log likelihood: -16142.627685
EM: Round [978] log likelihood: -16142.627348
EM: Round [979] log likelihood: -16142.627012
EM: Round [980] log likelihood: -16142.626677
EM: Round [981] log likelihood: -16142.626343
EM: Round [982] log likelihood: -16142.626010
EM: Round [983] log likelihood: -16142.625678
EM: Round [984] log likelihood: -16142.625347
EM: Round [985] log likelihood: -16142.625017
EM: Round [986] log likelihood: -16142.624688
EM: Round [987] log likelihood: -16142.624360
EM: Round [988] log likelihood: -16142.624033
EM: Round [989] log likelihood: -16142.623706
EM: Round [990] log likelihood: -16142.623381
EM: Round [991] log likelihood: -16142.623057
EM: Round [992] log likelihood: -16142.622733
EM: Round [993] log likelihood: -16142.622410
EM: Round [994] log likelihood: -16142.622089
EM: Round [995] log likelihood: -16142.621768
EM: Round [996] log likelihood: -16142.621448
EM: Round [997] log likelihood: -16142.621129
EM: Round [998] log likelihood: -16142.620811
EM: Round [999] log likelihood: -16142.620494
EM: Round [1000] log likelihood: -16142.620178
EM: Round [1001] log likelihood: -16142.619862
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir
-done, see /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -13636.060313
EM: Round [1] log likelihood: -13633.130663
EM: Round [2] log likelihood: -13633.113418
EM: Round [3] log likelihood: -13633.099377
EM: Round [4] log likelihood: -13633.085561
EM: Round [5] log likelihood: -13633.071962
EM: Round [6] log likelihood: -13633.058574
EM: Round [7] log likelihood: -13633.045391
EM: Round [8] log likelihood: -13633.032406
EM: Round [9] log likelihood: -13633.019616
EM: Round [10] log likelihood: -13633.007013
EM: Round [11] log likelihood: -13632.994593
EM: Round [12] log likelihood: -13632.982352
EM: Round [13] log likelihood: -13632.970284
EM: Round [14] log likelihood: -13632.958385
EM: Round [15] log likelihood: -13632.946651
EM: Round [16] log likelihood: -13632.935078
EM: Round [17] log likelihood: -13632.923661
EM: Round [18] log likelihood: -13632.912397
EM: Round [19] log likelihood: -13632.901282
EM: Round [20] log likelihood: -13632.890312
EM: Round [21] log likelihood: -13632.879484
EM: Round [22] log likelihood: -13632.868795
EM: Round [23] log likelihood: -13632.858241
EM: Round [24] log likelihood: -13632.847819
EM: Round [25] log likelihood: -13632.837527
EM: Round [26] log likelihood: -13632.827361
EM: Round [27] log likelihood: -13632.817319
EM: Round [28] log likelihood: -13632.807397
EM: Round [29] log likelihood: -13632.797594
EM: Round [30] log likelihood: -13632.787906
EM: Round [31] log likelihood: -13632.778332
EM: Round [32] log likelihood: -13632.768869
EM: Round [33] log likelihood: -13632.759514
EM: Round [34] log likelihood: -13632.750265
EM: Round [35] log likelihood: -13632.741120
EM: Round [36] log likelihood: -13632.732078
EM: Round [37] log likelihood: -13632.723135
EM: Round [38] log likelihood: -13632.714291
EM: Round [39] log likelihood: -13632.705542
EM: Round [40] log likelihood: -13632.696888
EM: Round [41] log likelihood: -13632.688326
EM: Round [42] log likelihood: -13632.679855
EM: Round [43] log likelihood: -13632.671472
EM: Round [44] log likelihood: -13632.663177
EM: Round [45] log likelihood: -13632.654968
EM: Round [46] log likelihood: -13632.646842
EM: Round [47] log likelihood: -13632.638799
EM: Round [48] log likelihood: -13632.630838
EM: Round [49] log likelihood: -13632.622955
EM: Round [50] log likelihood: -13632.615151
EM: Round [51] log likelihood: -13632.607424
EM: Round [52] log likelihood: -13632.599772
EM: Round [53] log likelihood: -13632.592195
EM: Round [54] log likelihood: -13632.584690
EM: Round [55] log likelihood: -13632.577257
EM: Round [56] log likelihood: -13632.569894
EM: Round [57] log likelihood: -13632.562601
EM: Round [58] log likelihood: -13632.555376
EM: Round [59] log likelihood: -13632.548218
EM: Round [60] log likelihood: -13632.541125
EM: Round [61] log likelihood: -13632.534098
EM: Round [62] log likelihood: -13632.527134
EM: Round [63] log likelihood: -13632.520234
EM: Round [64] log likelihood: -13632.513395
EM: Round [65] log likelihood: -13632.506616
EM: Round [66] log likelihood: -13632.499898
EM: Round [67] log likelihood: -13632.493239
EM: Round [68] log likelihood: -13632.486637
EM: Round [69] log likelihood: -13632.480093
EM: Round [70] log likelihood: -13632.473605
EM: Round [71] log likelihood: -13632.467173
EM: Round [72] log likelihood: -13632.460795
EM: Round [73] log likelihood: -13632.454471
EM: Round [74] log likelihood: -13632.448200
EM: Round [75] log likelihood: -13632.441982
EM: Round [76] log likelihood: -13632.435815
EM: Round [77] log likelihood: -13632.429698
EM: Round [78] log likelihood: -13632.423632
EM: Round [79] log likelihood: -13632.417615
EM: Round [80] log likelihood: -13632.411647
EM: Round [81] log likelihood: -13632.405727
EM: Round [82] log likelihood: -13632.399854
EM: Round [83] log likelihood: -13632.394027
EM: Round [84] log likelihood: -13632.388247
EM: Round [85] log likelihood: -13632.382512
EM: Round [86] log likelihood: -13632.376822
EM: Round [87] log likelihood: -13632.371176
EM: Round [88] log likelihood: -13632.365573
EM: Round [89] log likelihood: -13632.360014
EM: Round [90] log likelihood: -13632.354497
EM: Round [91] log likelihood: -13632.349022
EM: Round [92] log likelihood: -13632.343588
EM: Round [93] log likelihood: -13632.338195
EM: Round [94] log likelihood: -13632.332843
EM: Round [95] log likelihood: -13632.327530
EM: Round [96] log likelihood: -13632.322256
EM: Round [97] log likelihood: -13632.317021
EM: Round [98] log likelihood: -13632.311825
EM: Round [99] log likelihood: -13632.306666
EM: Round [100] log likelihood: -13632.301545
EM: Round [101] log likelihood: -13632.296460
EM: Round [102] log likelihood: -13632.291412
EM: Round [103] log likelihood: -13632.286400
EM: Round [104] log likelihood: -13632.281423
EM: Round [105] log likelihood: -13632.276482
EM: Round [106] log likelihood: -13632.271575
EM: Round [107] log likelihood: -13632.266703
EM: Round [108] log likelihood: -13632.261865
EM: Round [109] log likelihood: -13632.257060
EM: Round [110] log likelihood: -13632.252288
EM: Round [111] log likelihood: -13632.247549
EM: Round [112] log likelihood: -13632.242842
EM: Round [113] log likelihood: -13632.238167
EM: Round [114] log likelihood: -13632.233524
EM: Round [115] log likelihood: -13632.228912
EM: Round [116] log likelihood: -13632.224331
EM: Round [117] log likelihood: -13632.219780
EM: Round [118] log likelihood: -13632.215260
EM: Round [119] log likelihood: -13632.210769
EM: Round [120] log likelihood: -13632.206308
EM: Round [121] log likelihood: -13632.201877
EM: Round [122] log likelihood: -13632.197474
EM: Round [123] log likelihood: -13632.193100
EM: Round [124] log likelihood: -13632.188754
EM: Round [125] log likelihood: -13632.184436
EM: Round [126] log likelihood: -13632.180146
EM: Round [127] log likelihood: -13632.175883
EM: Round [128] log likelihood: -13632.171647
EM: Round [129] log likelihood: -13632.167438
EM: Round [130] log likelihood: -13632.163255
EM: Round [131] log likelihood: -13632.159099
EM: Round [132] log likelihood: -13632.154969
EM: Round [133] log likelihood: -13632.150864
EM: Round [134] log likelihood: -13632.146785
EM: Round [135] log likelihood: -13632.142731
EM: Round [136] log likelihood: -13632.138702
EM: Round [137] log likelihood: -13632.134698
EM: Round [138] log likelihood: -13632.130718
EM: Round [139] log likelihood: -13632.126762
EM: Round [140] log likelihood: -13632.122830
EM: Round [141] log likelihood: -13632.118922
EM: Round [142] log likelihood: -13632.115038
EM: Round [143] log likelihood: -13632.111176
EM: Round [144] log likelihood: -13632.107338
EM: Round [145] log likelihood: -13632.103522
EM: Round [146] log likelihood: -13632.099729
EM: Round [147] log likelihood: -13632.095958
EM: Round [148] log likelihood: -13632.092210
EM: Round [149] log likelihood: -13632.088483
EM: Round [150] log likelihood: -13632.084778
EM: Round [151] log likelihood: -13632.081095
EM: Round [152] log likelihood: -13632.077432
EM: Round [153] log likelihood: -13632.073791
EM: Round [154] log likelihood: -13632.070171
EM: Round [155] log likelihood: -13632.066572
EM: Round [156] log likelihood: -13632.062993
EM: Round [157] log likelihood: -13632.059434
EM: Round [158] log likelihood: -13632.055895
EM: Round [159] log likelihood: -13632.052377
EM: Round [160] log likelihood: -13632.048878
EM: Round [161] log likelihood: -13632.045399
EM: Round [162] log likelihood: -13632.041939
EM: Round [163] log likelihood: -13632.038498
EM: Round [164] log likelihood: -13632.035077
EM: Round [165] log likelihood: -13632.031674
EM: Round [166] log likelihood: -13632.028290
EM: Round [167] log likelihood: -13632.024925
EM: Round [168] log likelihood: -13632.021578
EM: Round [169] log likelihood: -13632.018249
EM: Round [170] log likelihood: -13632.014939
EM: Round [171] log likelihood: -13632.011646
EM: Round [172] log likelihood: -13632.008371
EM: Round [173] log likelihood: -13632.005114
EM: Round [174] log likelihood: -13632.001874
EM: Round [175] log likelihood: -13631.998651
EM: Round [176] log likelihood: -13631.995446
EM: Round [177] log likelihood: -13631.992258
EM: Round [178] log likelihood: -13631.989086
EM: Round [179] log likelihood: -13631.985931
EM: Round [180] log likelihood: -13631.982793
EM: Round [181] log likelihood: -13631.979671
EM: Round [182] log likelihood: -13631.976566
EM: Round [183] log likelihood: -13631.973477
EM: Round [184] log likelihood: -13631.970403
EM: Round [185] log likelihood: -13631.967346
EM: Round [186] log likelihood: -13631.964305
EM: Round [187] log likelihood: -13631.961279
EM: Round [188] log likelihood: -13631.958268
EM: Round [189] log likelihood: -13631.955273
EM: Round [190] log likelihood: -13631.952294
EM: Round [191] log likelihood: -13631.949329
EM: Round [192] log likelihood: -13631.946380
EM: Round [193] log likelihood: -13631.943445
EM: Round [194] log likelihood: -13631.940525
EM: Round [195] log likelihood: -13631.937620
EM: Round [196] log likelihood: -13631.934730
EM: Round [197] log likelihood: -13631.931853
EM: Round [198] log likelihood: -13631.928992
EM: Round [199] log likelihood: -13631.926144
EM: Round [200] log likelihood: -13631.923311
EM: Round [201] log likelihood: -13631.920491
EM: Round [202] log likelihood: -13631.917685
EM: Round [203] log likelihood: -13631.914894
EM: Round [204] log likelihood: -13631.912115
EM: Round [205] log likelihood: -13631.909351
EM: Round [206] log likelihood: -13631.906600
EM: Round [207] log likelihood: -13631.903862
EM: Round [208] log likelihood: -13631.901138
EM: Round [209] log likelihood: -13631.898426
EM: Round [210] log likelihood: -13631.895728
EM: Round [211] log likelihood: -13631.893043
EM: Round [212] log likelihood: -13631.890370
EM: Round [213] log likelihood: -13631.887711
EM: Round [214] log likelihood: -13631.885064
EM: Round [215] log likelihood: -13631.882429
EM: Round [216] log likelihood: -13631.879807
EM: Round [217] log likelihood: -13631.877198
EM: Round [218] log likelihood: -13631.874601
EM: Round [219] log likelihood: -13631.872016
EM: Round [220] log likelihood: -13631.869443
EM: Round [221] log likelihood: -13631.866882
EM: Round [222] log likelihood: -13631.864333
EM: Round [223] log likelihood: -13631.861796
EM: Round [224] log likelihood: -13631.859271
EM: Round [225] log likelihood: -13631.856758
EM: Round [226] log likelihood: -13631.854256
EM: Round [227] log likelihood: -13631.851766
EM: Round [228] log likelihood: -13631.849287
EM: Round [229] log likelihood: -13631.846819
EM: Round [230] log likelihood: -13631.844363
EM: Round [231] log likelihood: -13631.841918
EM: Round [232] log likelihood: -13631.839484
EM: Round [233] log likelihood: -13631.837062
EM: Round [234] log likelihood: -13631.834650
EM: Round [235] log likelihood: -13631.832249
EM: Round [236] log likelihood: -13631.829859
EM: Round [237] log likelihood: -13631.827480
EM: Round [238] log likelihood: -13631.825111
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EM: Round [700] log likelihood: -13631.297180
EM: Round [701] log likelihood: -13631.296658
EM: Round [702] log likelihood: -13631.296138
EM: Round [703] log likelihood: -13631.295619
EM: Round [704] log likelihood: -13631.295102
EM: Round [705] log likelihood: -13631.294586
EM: Round [706] log likelihood: -13631.294071
EM: Round [707] log likelihood: -13631.293558
EM: Round [708] log likelihood: -13631.293046
EM: Round [709] log likelihood: -13631.292536
EM: Round [710] log likelihood: -13631.292026
EM: Round [711] log likelihood: -13631.291519
EM: Round [712] log likelihood: -13631.291012
EM: Round [713] log likelihood: -13631.290507
EM: Round [714] log likelihood: -13631.290003
EM: Round [715] log likelihood: -13631.289500
EM: Round [716] log likelihood: -13631.288999
EM: Round [717] log likelihood: -13631.288499
EM: Round [718] log likelihood: -13631.288001
EM: Round [719] log likelihood: -13631.287503
EM: Round [720] log likelihood: -13631.287007
EM: Round [721] log likelihood: -13631.286513
EM: Round [722] log likelihood: -13631.286019
EM: Round [723] log likelihood: -13631.285527
EM: Round [724] log likelihood: -13631.285036
EM: Round [725] log likelihood: -13631.284547
EM: Round [726] log likelihood: -13631.284058
EM: Round [727] log likelihood: -13631.283571
EM: Round [728] log likelihood: -13631.283086
EM: Round [729] log likelihood: -13631.282601
EM: Round [730] log likelihood: -13631.282118
EM: Round [731] log likelihood: -13631.281636
EM: Round [732] log likelihood: -13631.281155
EM: Round [733] log likelihood: -13631.280676
EM: Round [734] log likelihood: -13631.280198
EM: Round [735] log likelihood: -13631.279721
EM: Round [736] log likelihood: -13631.279245
EM: Round [737] log likelihood: -13631.278771
EM: Round [738] log likelihood: -13631.278297
EM: Round [739] log likelihood: -13631.277825
EM: Round [740] log likelihood: -13631.277355
EM: Round [741] log likelihood: -13631.276885
EM: Round [742] log likelihood: -13631.276417
EM: Round [743] log likelihood: -13631.275950
EM: Round [744] log likelihood: -13631.275484
EM: Round [745] log likelihood: -13631.275019
EM: Round [746] log likelihood: -13631.274555
EM: Round [747] log likelihood: -13631.274093
EM: Round [748] log likelihood: -13631.273632
EM: Round [749] log likelihood: -13631.273172
EM: Round [750] log likelihood: -13631.272713
EM: Round [751] log likelihood: -13631.272256
EM: Round [752] log likelihood: -13631.271799
EM: Round [753] log likelihood: -13631.271344
EM: Round [754] log likelihood: -13631.270890
EM: Round [755] log likelihood: -13631.270437
EM: Round [756] log likelihood: -13631.269985
EM: Round [757] log likelihood: -13631.269535
EM: Round [758] log likelihood: -13631.269086
EM: Round [759] log likelihood: -13631.268637
EM: Round [760] log likelihood: -13631.268190
EM: Round [761] log likelihood: -13631.267744
EM: Round [762] log likelihood: -13631.267300
EM: Round [763] log likelihood: -13631.266856
EM: Round [764] log likelihood: -13631.266413
EM: Round [765] log likelihood: -13631.265972
EM: Round [766] log likelihood: -13631.265532
EM: Round [767] log likelihood: -13631.265093
EM: Round [768] log likelihood: -13631.264655
EM: Round [769] log likelihood: -13631.264218
EM: Round [770] log likelihood: -13631.263782
EM: Round [771] log likelihood: -13631.263347
EM: Round [772] log likelihood: -13631.262914
EM: Round [773] log likelihood: -13631.262481
EM: Round [774] log likelihood: -13631.262050
EM: Round [775] log likelihood: -13631.261620
EM: Round [776] log likelihood: -13631.261191
EM: Round [777] log likelihood: -13631.260763
EM: Round [778] log likelihood: -13631.260336
EM: Round [779] log likelihood: -13631.259910
EM: Round [780] log likelihood: -13631.259485
EM: Round [781] log likelihood: -13631.259062
EM: Round [782] log likelihood: -13631.258639
EM: Round [783] log likelihood: -13631.258218
EM: Round [784] log likelihood: -13631.257797
EM: Round [785] log likelihood: -13631.257378
EM: Round [786] log likelihood: -13631.256959
EM: Round [787] log likelihood: -13631.256542
EM: Round [788] log likelihood: -13631.256126
EM: Round [789] log likelihood: -13631.255711
EM: Round [790] log likelihood: -13631.255297
EM: Round [791] log likelihood: -13631.254884
EM: Round [792] log likelihood: -13631.254472
EM: Round [793] log likelihood: -13631.254061
EM: Round [794] log likelihood: -13631.253651
EM: Round [795] log likelihood: -13631.253242
EM: Round [796] log likelihood: -13631.252834
EM: Round [797] log likelihood: -13631.252427
EM: Round [798] log likelihood: -13631.252022
EM: Round [799] log likelihood: -13631.251617
EM: Round [800] log likelihood: -13631.251213
EM: Round [801] log likelihood: -13631.250811
EM: Round [802] log likelihood: -13631.250409
EM: Round [803] log likelihood: -13631.250008
EM: Round [804] log likelihood: -13631.249609
EM: Round [805] log likelihood: -13631.249210
EM: Round [806] log likelihood: -13631.248812
EM: Round [807] log likelihood: -13631.248416
EM: Round [808] log likelihood: -13631.248020
EM: Round [809] log likelihood: -13631.247625
EM: Round [810] log likelihood: -13631.247232
EM: Round [811] log likelihood: -13631.246839
EM: Round [812] log likelihood: -13631.246447
EM: Round [813] log likelihood: -13631.246057
EM: Round [814] log likelihood: -13631.245667
EM: Round [815] log likelihood: -13631.245278
EM: Round [816] log likelihood: -13631.244890
EM: Round [817] log likelihood: -13631.244504
EM: Round [818] log likelihood: -13631.244118
EM: Round [819] log likelihood: -13631.243733
EM: Round [820] log likelihood: -13631.243349
EM: Round [821] log likelihood: -13631.242966
EM: Round [822] log likelihood: -13631.242584
EM: Round [823] log likelihood: -13631.242203
EM: Round [824] log likelihood: -13631.241823
EM: Round [825] log likelihood: -13631.241444
EM: Round [826] log likelihood: -13631.241066
EM: Round [827] log likelihood: -13631.240689
EM: Round [828] log likelihood: -13631.240312
EM: Round [829] log likelihood: -13631.239937
EM: Round [830] log likelihood: -13631.239563
EM: Round [831] log likelihood: -13631.239189
EM: Round [832] log likelihood: -13631.238817
EM: Round [833] log likelihood: -13631.238445
EM: Round [834] log likelihood: -13631.238075
EM: Round [835] log likelihood: -13631.237705
EM: Round [836] log likelihood: -13631.237336
EM: Round [837] log likelihood: -13631.236968
EM: Round [838] log likelihood: -13631.236601
EM: Round [839] log likelihood: -13631.236235
EM: Round [840] log likelihood: -13631.235870
EM: Round [841] log likelihood: -13631.235506
EM: Round [842] log likelihood: -13631.235142
EM: Round [843] log likelihood: -13631.234780
EM: Round [844] log likelihood: -13631.234418
EM: Round [845] log likelihood: -13631.234058
EM: Round [846] log likelihood: -13631.233698
EM: Round [847] log likelihood: -13631.233339
EM: Round [848] log likelihood: -13631.232981
EM: Round [849] log likelihood: -13631.232624
EM: Round [850] log likelihood: -13631.232268
EM: Round [851] log likelihood: -13631.231913
EM: Round [852] log likelihood: -13631.231558
EM: Round [853] log likelihood: -13631.231205
EM: Round [854] log likelihood: -13631.230852
EM: Round [855] log likelihood: -13631.230500
EM: Round [856] log likelihood: -13631.230149
EM: Round [857] log likelihood: -13631.229799
EM: Round [858] log likelihood: -13631.229450
EM: Round [859] log likelihood: -13631.229102
EM: Round [860] log likelihood: -13631.228754
EM: Round [861] log likelihood: -13631.228407
EM: Round [862] log likelihood: -13631.228062
EM: Round [863] log likelihood: -13631.227717
EM: Round [864] log likelihood: -13631.227373
EM: Round [865] log likelihood: -13631.227029
EM: Round [866] log likelihood: -13631.226687
EM: Round [867] log likelihood: -13631.226346
EM: Round [868] log likelihood: -13631.226005
EM: Round [869] log likelihood: -13631.225665
EM: Round [870] log likelihood: -13631.225326
EM: Round [871] log likelihood: -13631.224988
EM: Round [872] log likelihood: -13631.224651
EM: Round [873] log likelihood: -13631.224314
EM: Round [874] log likelihood: -13631.223978
EM: Round [875] log likelihood: -13631.223644
EM: Round [876] log likelihood: -13631.223309
EM: Round [877] log likelihood: -13631.222976
EM: Round [878] log likelihood: -13631.222644
EM: Round [879] log likelihood: -13631.222312
EM: Round [880] log likelihood: -13631.221982
EM: Round [881] log likelihood: -13631.221652
EM: Round [882] log likelihood: -13631.221322
EM: Round [883] log likelihood: -13631.220994
EM: Round [884] log likelihood: -13631.220667
EM: Round [885] log likelihood: -13631.220340
EM: Round [886] log likelihood: -13631.220014
EM: Round [887] log likelihood: -13631.219689
EM: Round [888] log likelihood: -13631.219364
EM: Round [889] log likelihood: -13631.219041
EM: Round [890] log likelihood: -13631.218718
EM: Round [891] log likelihood: -13631.218396
EM: Round [892] log likelihood: -13631.218075
EM: Round [893] log likelihood: -13631.217755
EM: Round [894] log likelihood: -13631.217435
EM: Round [895] log likelihood: -13631.217116
EM: Round [896] log likelihood: -13631.216798
EM: Round [897] log likelihood: -13631.216481
EM: Round [898] log likelihood: -13631.216164
EM: Round [899] log likelihood: -13631.215849
EM: Round [900] log likelihood: -13631.215534
EM: Round [901] log likelihood: -13631.215219
EM: Round [902] log likelihood: -13631.214906
EM: Round [903] log likelihood: -13631.214593
EM: Round [904] log likelihood: -13631.214281
EM: Round [905] log likelihood: -13631.213970
EM: Round [906] log likelihood: -13631.213660
EM: Round [907] log likelihood: -13631.213350
EM: Round [908] log likelihood: -13631.213041
EM: Round [909] log likelihood: -13631.212733
EM: Round [910] log likelihood: -13631.212426
EM: Round [911] log likelihood: -13631.212119
EM: Round [912] log likelihood: -13631.211813
EM: Round [913] log likelihood: -13631.211508
EM: Round [914] log likelihood: -13631.211204
EM: Round [915] log likelihood: -13631.210900
EM: Round [916] log likelihood: -13631.210597
EM: Round [917] log likelihood: -13631.210295
EM: Round [918] log likelihood: -13631.209994
EM: Round [919] log likelihood: -13631.209693
EM: Round [920] log likelihood: -13631.209393
EM: Round [921] log likelihood: -13631.209094
EM: Round [922] log likelihood: -13631.208795
EM: Round [923] log likelihood: -13631.208497
EM: Round [924] log likelihood: -13631.208200
EM: Round [925] log likelihood: -13631.207904
EM: Round [926] log likelihood: -13631.207608
EM: Round [927] log likelihood: -13631.207313
EM: Round [928] log likelihood: -13631.207019
EM: Round [929] log likelihood: -13631.206725
EM: Round [930] log likelihood: -13631.206432
EM: Round [931] log likelihood: -13631.206140
EM: Round [932] log likelihood: -13631.205849
EM: Round [933] log likelihood: -13631.205558
EM: Round [934] log likelihood: -13631.205268
EM: Round [935] log likelihood: -13631.204979
EM: Round [936] log likelihood: -13631.204690
EM: Round [937] log likelihood: -13631.204402
EM: Round [938] log likelihood: -13631.204115
EM: Round [939] log likelihood: -13631.203829
EM: Round [940] log likelihood: -13631.203543
EM: Round [941] log likelihood: -13631.203258
EM: Round [942] log likelihood: -13631.202973
EM: Round [943] log likelihood: -13631.202689
EM: Round [944] log likelihood: -13631.202406
EM: Round [945] log likelihood: -13631.202124
EM: Round [946] log likelihood: -13631.201842
EM: Round [947] log likelihood: -13631.201561
EM: Round [948] log likelihood: -13631.201281
EM: Round [949] log likelihood: -13631.201001
EM: Round [950] log likelihood: -13631.200722
EM: Round [951] log likelihood: -13631.200444
EM: Round [952] log likelihood: -13631.200166
EM: Round [953] log likelihood: -13631.199889
EM: Round [954] log likelihood: -13631.199612
EM: Round [955] log likelihood: -13631.199337
EM: Round [956] log likelihood: -13631.199062
EM: Round [957] log likelihood: -13631.198787
EM: Round [958] log likelihood: -13631.198514
EM: Round [959] log likelihood: -13631.198241
EM: Round [960] log likelihood: -13631.197968
EM: Round [961] log likelihood: -13631.197696
EM: Round [962] log likelihood: -13631.197425
EM: Round [963] log likelihood: -13631.197155
EM: Round [964] log likelihood: -13631.196885
EM: Round [965] log likelihood: -13631.196616
EM: Round [966] log likelihood: -13631.196347
EM: Round [967] log likelihood: -13631.196079
EM: Round [968] log likelihood: -13631.195812
EM: Round [969] log likelihood: -13631.195546
EM: Round [970] log likelihood: -13631.195280
EM: Round [971] log likelihood: -13631.195014
EM: Round [972] log likelihood: -13631.194749
EM: Round [973] log likelihood: -13631.194485
EM: Round [974] log likelihood: -13631.194222
EM: Round [975] log likelihood: -13631.193959
EM: Round [976] log likelihood: -13631.193697
EM: Round [977] log likelihood: -13631.193435
EM: Round [978] log likelihood: -13631.193174
EM: Round [979] log likelihood: -13631.192914
EM: Round [980] log likelihood: -13631.192654
EM: Round [981] log likelihood: -13631.192395
EM: Round [982] log likelihood: -13631.192137
EM: Round [983] log likelihood: -13631.191879
EM: Round [984] log likelihood: -13631.191622
EM: Round [985] log likelihood: -13631.191365
EM: Round [986] log likelihood: -13631.191109
EM: Round [987] log likelihood: -13631.190854
EM: Round [988] log likelihood: -13631.190599
EM: Round [989] log likelihood: -13631.190345
EM: Round [990] log likelihood: -13631.190091
EM: Round [991] log likelihood: -13631.189838
EM: Round [992] log likelihood: -13631.189586
EM: Round [993] log likelihood: -13631.189334
EM: Round [994] log likelihood: -13631.189083
EM: Round [995] log likelihood: -13631.188832
EM: Round [996] log likelihood: -13631.188582
EM: Round [997] log likelihood: -13631.188333
EM: Round [998] log likelihood: -13631.188084
EM: Round [999] log likelihood: -13631.187836
EM: Round [1000] log likelihood: -13631.187588
EM: Round [1001] log likelihood: -13631.187341
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296334011
Execution Time = 5.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.EVTZxZ8xgB/fi_workdir/microH.dat
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.EVTZxZ8xgB/fi_workdir/microH.dat /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/fi_workdir/microH.dat /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.EVTZxZ8xgB --json_outfile /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_Fr-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.EVTZxZ8xgB --json_outfile /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_Fr-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.EVTZxZ8xgB/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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_Fr-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_Fr-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-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.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000276462.2]
WARNING, no entry stored in dbm for [ENSG00000276462.2]
WARNING, no entry stored in dbm for [ENSG00000276462.2]
WARNING, no entry stored in dbm for [ENSG00000234768.1]
WARNING, no entry stored in dbm for [ENSG00000234768.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000286593.1]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000270157.1]
WARNING, no entry stored in dbm for [ENSG00000270157.1]
WARNING, no entry stored in dbm for [ENSG00000203739.4]
WARNING, no entry stored in dbm for [ENSG00000235578.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.EVTZxZ8xgB/ctat_genome_lib_build_dir > /tmp/nxf.EVTZxZ8xgB/659_Fr-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.EVTZxZ8xgB/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory