Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/b6db2a2c5a0fd295af2e76270cb410/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/6b4377a197facd366c297e0310f554/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/6b4377a197facd366c297e0310f554/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d24ff6626699d15295e922fa65d375/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d24ff6626699d15295e922fa65d375/659_cIX-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/cytoBand.txt
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.i1B8rRXG8j/fi_workdir --reads "/tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:54:58 ..... started STAR run
Jun 08 09:54:58 ..... loading genome
Jun 08 09:56:49 ... generating Suffix Array index
Jun 08 10:00:42 ... completed Suffix Array index
Jun 08 10:00:43 ..... processing annotations GTF
Jun 08 10:00:43 ..... inserting junctions into the genome indices
Jun 08 10:01:44 ..... started mapping
Jun 08 11:16:56 ..... finished mapping
Jun 08 11:16:58 ..... started sorting BAM
Jun 08 11:16:59 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 82.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.i1B8rRXG8j/fi_workdir --reads "/tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:17:09 : INFO : Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[1710000] -done parsing /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 231,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'low complexity anchor region' => 1,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num genes matched < 2' => 44,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 38,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
' ** passed ** ' => 9658,
'small anchor length' => 119,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 251,
'excessive soft clipping' => 9567,
'per_id < 96' => 7261
};
-writing fusion junction support info.
Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[50000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[43000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[21000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[39000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[46000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[1144000] -fusion SPANNING read extraction for scaff: TNS1--ALK
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 55828,
'lacks exon overlap' => 4308
};
Execution Time = 2.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -5303.008241
EM: Round [1] log likelihood: -5299.278672
EM: Round [2] log likelihood: -5299.228764
EM: Round [3] log likelihood: -5299.199553
EM: Round [4] log likelihood: -5299.171896
EM: Round [5] log likelihood: -5299.144917
EM: Round [6] log likelihood: -5299.118555
EM: Round [7] log likelihood: -5299.092790
EM: Round [8] log likelihood: -5299.067604
EM: Round [9] log likelihood: -5299.042980
EM: Round [10] log likelihood: -5299.018901
EM: Round [11] log likelihood: -5298.995351
EM: Round [12] log likelihood: -5298.972314
EM: Round [13] log likelihood: -5298.949777
EM: Round [14] log likelihood: -5298.927724
EM: Round [15] log likelihood: -5298.906142
EM: Round [16] log likelihood: -5298.885018
EM: Round [17] log likelihood: -5298.864339
EM: Round [18] log likelihood: -5298.844094
EM: Round [19] log likelihood: -5298.824271
EM: Round [20] log likelihood: -5298.804857
EM: Round [21] log likelihood: -5298.785843
EM: Round [22] log likelihood: -5298.767218
EM: Round [23] log likelihood: -5298.748972
EM: Round [24] log likelihood: -5298.731095
EM: Round [25] log likelihood: -5298.713578
EM: Round [26] log likelihood: -5298.696411
EM: Round [27] log likelihood: -5298.679586
EM: Round [28] log likelihood: -5298.663094
EM: Round [29] log likelihood: -5298.646926
EM: Round [30] log likelihood: -5298.631076
EM: Round [31] log likelihood: -5298.615535
EM: Round [32] log likelihood: -5298.600296
EM: Round [33] log likelihood: -5298.585351
EM: Round [34] log likelihood: -5298.570694
EM: Round [35] log likelihood: -5298.556317
EM: Round [36] log likelihood: -5298.542215
EM: Round [37] log likelihood: -5298.528380
EM: Round [38] log likelihood: -5298.514806
EM: Round [39] log likelihood: -5298.501489
EM: Round [40] log likelihood: -5298.488420
EM: Round [41] log likelihood: -5298.475596
EM: Round [42] log likelihood: -5298.463010
EM: Round [43] log likelihood: -5298.450657
EM: Round [44] log likelihood: -5298.438532
EM: Round [45] log likelihood: -5298.426630
EM: Round [46] log likelihood: -5298.414945
EM: Round [47] log likelihood: -5298.403474
EM: Round [48] log likelihood: -5298.392211
EM: Round [49] log likelihood: -5298.381153
EM: Round [50] log likelihood: -5298.370293
EM: Round [51] log likelihood: -5298.359629
EM: Round [52] log likelihood: -5298.349157
EM: Round [53] log likelihood: -5298.338871
EM: Round [54] log likelihood: -5298.328768
EM: Round [55] log likelihood: -5298.318845
EM: Round [56] log likelihood: -5298.309097
EM: Round [57] log likelihood: -5298.299521
EM: Round [58] log likelihood: -5298.290113
EM: Round [59] log likelihood: -5298.280870
EM: Round [60] log likelihood: -5298.271789
EM: Round [61] log likelihood: -5298.262866
EM: Round [62] log likelihood: -5298.254097
EM: Round [63] log likelihood: -5298.245481
EM: Round [64] log likelihood: -5298.237013
EM: Round [65] log likelihood: -5298.228691
EM: Round [66] log likelihood: -5298.220512
EM: Round [67] log likelihood: -5298.212473
EM: Round [68] log likelihood: -5298.204571
EM: Round [69] log likelihood: -5298.196804
EM: Round [70] log likelihood: -5298.189169
EM: Round [71] log likelihood: -5298.181663
EM: Round [72] log likelihood: -5298.174284
EM: Round [73] log likelihood: -5298.167029
EM: Round [74] log likelihood: -5298.159896
EM: Round [75] log likelihood: -5298.152883
EM: Round [76] log likelihood: -5298.145987
EM: Round [77] log likelihood: -5298.139206
EM: Round [78] log likelihood: -5298.132538
EM: Round [79] log likelihood: -5298.125981
EM: Round [80] log likelihood: -5298.119532
EM: Round [81] log likelihood: -5298.113190
EM: Round [82] log likelihood: -5298.106952
EM: Round [83] log likelihood: -5298.100818
EM: Round [84] log likelihood: -5298.094783
EM: Round [85] log likelihood: -5298.088848
EM: Round [86] log likelihood: -5298.083010
EM: Round [87] log likelihood: -5298.077267
EM: Round [88] log likelihood: -5298.071617
EM: Round [89] log likelihood: -5298.066059
EM: Round [90] log likelihood: -5298.060592
EM: Round [91] log likelihood: -5298.055212
EM: Round [92] log likelihood: -5298.049920
EM: Round [93] log likelihood: -5298.044712
EM: Round [94] log likelihood: -5298.039589
EM: Round [95] log likelihood: -5298.034547
EM: Round [96] log likelihood: -5298.029587
EM: Round [97] log likelihood: -5298.024705
EM: Round [98] log likelihood: -5298.019901
EM: Round [99] log likelihood: -5298.015174
EM: Round [100] log likelihood: -5298.010522
EM: Round [101] log likelihood: -5298.005944
EM: Round [102] log likelihood: -5298.001438
EM: Round [103] log likelihood: -5297.997003
EM: Round [104] log likelihood: -5297.992639
EM: Round [105] log likelihood: -5297.988343
EM: Round [106] log likelihood: -5297.984114
EM: Round [107] log likelihood: -5297.979952
EM: Round [108] log likelihood: -5297.975855
EM: Round [109] log likelihood: -5297.971822
EM: Round [110] log likelihood: -5297.967852
EM: Round [111] log likelihood: -5297.963944
EM: Round [112] log likelihood: -5297.960096
EM: Round [113] log likelihood: -5297.956308
EM: Round [114] log likelihood: -5297.952579
EM: Round [115] log likelihood: -5297.948908
EM: Round [116] log likelihood: -5297.945293
EM: Round [117] log likelihood: -5297.941734
EM: Round [118] log likelihood: -5297.938230
EM: Round [119] log likelihood: -5297.934780
EM: Round [120] log likelihood: -5297.931382
EM: Round [121] log likelihood: -5297.928037
EM: Round [122] log likelihood: -5297.924743
EM: Round [123] log likelihood: -5297.921499
EM: Round [124] log likelihood: -5297.918305
EM: Round [125] log likelihood: -5297.915159
EM: Round [126] log likelihood: -5297.912061
EM: Round [127] log likelihood: -5297.909010
EM: Round [128] log likelihood: -5297.906005
EM: Round [129] log likelihood: -5297.903046
EM: Round [130] log likelihood: -5297.900132
EM: Round [131] log likelihood: -5297.897261
EM: Round [132] log likelihood: -5297.894434
EM: Round [133] log likelihood: -5297.891649
EM: Round [134] log likelihood: -5297.888906
EM: Round [135] log likelihood: -5297.886205
EM: Round [136] log likelihood: -5297.883543
EM: Round [137] log likelihood: -5297.880922
EM: Round [138] log likelihood: -5297.878340
EM: Round [139] log likelihood: -5297.875796
EM: Round [140] log likelihood: -5297.873290
EM: Round [141] log likelihood: -5297.870821
EM: Round [142] log likelihood: -5297.868389
EM: Round [143] log likelihood: -5297.865994
EM: Round [144] log likelihood: -5297.863633
EM: Round [145] log likelihood: -5297.861308
EM: Round [146] log likelihood: -5297.859017
EM: Round [147] log likelihood: -5297.856760
EM: Round [148] log likelihood: -5297.854536
EM: Round [149] log likelihood: -5297.852344
EM: Round [150] log likelihood: -5297.850185
EM: Round [151] log likelihood: -5297.848058
EM: Round [152] log likelihood: -5297.845962
EM: Round [153] log likelihood: -5297.843896
EM: Round [154] log likelihood: -5297.841861
EM: Round [155] log likelihood: -5297.839855
EM: Round [156] log likelihood: -5297.837879
EM: Round [157] log likelihood: -5297.835932
EM: Round [158] log likelihood: -5297.834012
EM: Round [159] log likelihood: -5297.832121
EM: Round [160] log likelihood: -5297.830257
EM: Round [161] log likelihood: -5297.828420
EM: Round [162] log likelihood: -5297.826610
EM: Round [163] log likelihood: -5297.824826
EM: Round [164] log likelihood: -5297.823068
EM: Round [165] log likelihood: -5297.821335
EM: Round [166] log likelihood: -5297.819627
EM: Round [167] log likelihood: -5297.817944
EM: Round [168] log likelihood: -5297.816285
EM: Round [169] log likelihood: -5297.814649
EM: Round [170] log likelihood: -5297.813037
EM: Round [171] log likelihood: -5297.811449
EM: Round [172] log likelihood: -5297.809882
EM: Round [173] log likelihood: -5297.808339
EM: Round [174] log likelihood: -5297.806817
EM: Round [175] log likelihood: -5297.805317
EM: Round [176] log likelihood: -5297.803839
EM: Round [177] log likelihood: -5297.802381
EM: Round [178] log likelihood: -5297.800944
EM: Round [179] log likelihood: -5297.799528
EM: Round [180] log likelihood: -5297.798132
EM: Round [181] log likelihood: -5297.796755
EM: Round [182] log likelihood: -5297.795398
EM: Round [183] log likelihood: -5297.794060
EM: Round [184] log likelihood: -5297.792741
EM: Round [185] log likelihood: -5297.791441
EM: Round [186] log likelihood: -5297.790159
EM: Round [187] log likelihood: -5297.788895
EM: Round [188] log likelihood: -5297.787648
EM: Round [189] log likelihood: -5297.786420
EM: Round [190] log likelihood: -5297.785208
EM: Round [191] log likelihood: -5297.784014
EM: Round [192] log likelihood: -5297.782836
EM: Round [193] log likelihood: -5297.781674
EM: Round [194] log likelihood: -5297.780529
EM: Round [195] log likelihood: -5297.779400
EM: Round [196] log likelihood: -5297.778287
EM: Round [197] log likelihood: -5297.777189
EM: Round [198] log likelihood: -5297.776106
EM: Round [199] log likelihood: -5297.775039
EM: Round [200] log likelihood: -5297.773986
EM: Round [201] log likelihood: -5297.772948
EM: Round [202] log likelihood: -5297.771924
EM: Round [203] log likelihood: -5297.770915
EM: Round [204] log likelihood: -5297.769919
EM: Round [205] log likelihood: -5297.768937
EM: Round [206] log likelihood: -5297.767969
EM: Round [207] log likelihood: -5297.767014
EM: Round [208] log likelihood: -5297.766072
EM: Round [209] log likelihood: -5297.765143
EM: Round [210] log likelihood: -5297.764227
EM: Round [211] log likelihood: -5297.763324
EM: Round [212] log likelihood: -5297.762433
EM: Round [213] log likelihood: -5297.761554
EM: Round [214] log likelihood: -5297.760687
EM: Round [215] log likelihood: -5297.759832
EM: Round [216] log likelihood: -5297.758989
EM: Round [217] log likelihood: -5297.758157
EM: Round [218] log likelihood: -5297.757337
EM: Round [219] log likelihood: -5297.756528
EM: Round [220] log likelihood: -5297.755730
EM: Round [221] log likelihood: -5297.754942
EM: Round [222] log likelihood: -5297.754166
EM: Round [223] log likelihood: -5297.753400
EM: Round [224] log likelihood: -5297.752644
EM: Round [225] log likelihood: -5297.751899
EM: Round [226] log likelihood: -5297.751163
EM: Round [227] log likelihood: -5297.750438
EM: Round [228] log likelihood: -5297.749723
EM: Round [229] log likelihood: -5297.749017
EM: Round [230] log likelihood: -5297.748320
EM: Round [231] log likelihood: -5297.747634
EM: Round [232] log likelihood: -5297.746956
EM: Round [233] log likelihood: -5297.746287
EM: Round [234] log likelihood: -5297.745628
EM: Round [235] log likelihood: -5297.744977
EM: Round [236] log likelihood: -5297.744335
EM: Round [237] log likelihood: -5297.743702
EM: Round [238] log likelihood: -5297.743077
EM: Round [239] log likelihood: -5297.742461
EM: Round [240] log likelihood: -5297.741853
EM: Round [241] log likelihood: -5297.741253
EM: Round [242] log likelihood: -5297.740661
EM: Round [243] log likelihood: -5297.740076
EM: Round [244] log likelihood: -5297.739500
EM: Round [245] log likelihood: -5297.738932
EM: Round [246] log likelihood: -5297.738370
EM: Round [247] log likelihood: -5297.737817
EM: Round [248] log likelihood: -5297.737271
EM: Round [249] log likelihood: -5297.736732
EM: Round [250] log likelihood: -5297.736200
EM: Round [251] log likelihood: -5297.735675
EM: Round [252] log likelihood: -5297.735157
EM: Round [253] log likelihood: -5297.734647
EM: Round [254] log likelihood: -5297.734142
EM: Round [255] log likelihood: -5297.733645
EM: Round [256] log likelihood: -5297.733154
EM: Round [257] log likelihood: -5297.732670
EM: Round [258] log likelihood: -5297.732192
EM: Round [259] log likelihood: -5297.731720
EM: Round [260] log likelihood: -5297.731254
EM: Round [261] log likelihood: -5297.730795
EM: Round [262] log likelihood: -5297.730342
EM: Round [263] log likelihood: -5297.729894
EM: Round [264] log likelihood: -5297.729453
EM: Round [265] log likelihood: -5297.729017
EM: Round [266] log likelihood: -5297.728587
EM: Round [267] log likelihood: -5297.728163
EM: Round [268] log likelihood: -5297.727744
EM: Round [269] log likelihood: -5297.727331
EM: Round [270] log likelihood: -5297.726923
EM: Round [271] log likelihood: -5297.726520
EM: Round [272] log likelihood: -5297.726123
EM: Round [273] log likelihood: -5297.725731
EM: Round [274] log likelihood: -5297.725344
EM: Round [275] log likelihood: -5297.724962
EM: Round [276] log likelihood: -5297.724585
EM: Round [277] log likelihood: -5297.724213
EM: Round [278] log likelihood: -5297.723846
EM: Round [279] log likelihood: -5297.723483
EM: Round [280] log likelihood: -5297.723126
EM: Round [281] log likelihood: -5297.722773
EM: Round [282] log likelihood: -5297.722424
EM: Round [283] log likelihood: -5297.722080
EM: Round [284] log likelihood: -5297.721741
EM: Round [285] log likelihood: -5297.721406
EM: Round [286] log likelihood: -5297.721075
EM: Round [287] log likelihood: -5297.720748
EM: Round [288] log likelihood: -5297.720426
EM: Round [289] log likelihood: -5297.720108
EM: Round [290] log likelihood: -5297.719794
EM: Round [291] log likelihood: -5297.719484
EM: Round [292] log likelihood: -5297.719178
EM: Round [293] log likelihood: -5297.718876
EM: Round [294] log likelihood: -5297.718578
EM: Round [295] log likelihood: -5297.718283
EM: Round [296] log likelihood: -5297.717993
EM: Round [297] log likelihood: -5297.717706
EM: Round [298] log likelihood: -5297.717423
EM: Round [299] log likelihood: -5297.717144
EM: Round [300] log likelihood: -5297.716868
EM: Round [301] log likelihood: -5297.716595
EM: Round [302] log likelihood: -5297.716326
EM: Round [303] log likelihood: -5297.716061
EM: Round [304] log likelihood: -5297.715799
EM: Round [305] log likelihood: -5297.715540
EM: Round [306] log likelihood: -5297.715285
EM: Round [307] log likelihood: -5297.715033
EM: Round [308] log likelihood: -5297.714784
EM: Round [309] log likelihood: -5297.714538
EM: Round [310] log likelihood: -5297.714296
EM: Round [311] log likelihood: -5297.714056
EM: Round [312] log likelihood: -5297.713820
EM: Round [313] log likelihood: -5297.713586
EM: Round [314] log likelihood: -5297.713356
EM: Round [315] log likelihood: -5297.713128
EM: Round [316] log likelihood: -5297.712904
EM: Round [317] log likelihood: -5297.712682
EM: Round [318] log likelihood: -5297.712463
EM: Round [319] log likelihood: -5297.712247
EM: Round [320] log likelihood: -5297.712033
EM: Round [321] log likelihood: -5297.711822
EM: Round [322] log likelihood: -5297.711614
EM: Round [323] log likelihood: -5297.711409
EM: Round [324] log likelihood: -5297.711206
EM: Round [325] log likelihood: -5297.711006
EM: Round [326] log likelihood: -5297.710808
EM: Round [327] log likelihood: -5297.710613
EM: Round [328] log likelihood: -5297.710420
EM: Round [329] log likelihood: -5297.710230
EM: Round [330] log likelihood: -5297.710042
EM: Round [331] log likelihood: -5297.709856
EM: Round [332] log likelihood: -5297.709673
EM: Round [333] log likelihood: -5297.709492
EM: Round [334] log likelihood: -5297.709313
EM: Round [335] log likelihood: -5297.709137
EM: Round [336] log likelihood: -5297.708963
EM: Round [337] log likelihood: -5297.708791
EM: Round [338] log likelihood: -5297.708621
EM: Round [339] log likelihood: -5297.708453
EM: Round [340] log likelihood: -5297.708287
EM: Round [341] log likelihood: -5297.708124
EM: Round [342] log likelihood: -5297.707962
EM: Round [343] log likelihood: -5297.707803
EM: Round [344] log likelihood: -5297.707645
EM: Round [345] log likelihood: -5297.707490
EM: Round [346] log likelihood: -5297.707336
EM: Round [347] log likelihood: -5297.707185
EM: Round [348] log likelihood: -5297.707035
EM: Round [349] log likelihood: -5297.706887
EM: Round [350] log likelihood: -5297.706741
EM: Round [351] log likelihood: -5297.706597
EM: Round [352] log likelihood: -5297.706455
EM: Round [353] log likelihood: -5297.706314
EM: Round [354] log likelihood: -5297.706175
EM: Round [355] log likelihood: -5297.706038
EM: Round [356] log likelihood: -5297.705902
EM: Round [357] log likelihood: -5297.705769
EM: Round [358] log likelihood: -5297.705637
EM: Round [359] log likelihood: -5297.705506
EM: Round [360] log likelihood: -5297.705377
EM: Round [361] log likelihood: -5297.705250
EM: Round [362] log likelihood: -5297.705124
EM: Round [363] log likelihood: -5297.705000
EM: Round [364] log likelihood: -5297.704878
EM: Round [365] log likelihood: -5297.704757
EM: Round [366] log likelihood: -5297.704637
EM: Round [367] log likelihood: -5297.704519
EM: Round [368] log likelihood: -5297.704403
EM: Round [369] log likelihood: -5297.704288
EM: Round [370] log likelihood: -5297.704174
EM: Round [371] log likelihood: -5297.704062
EM: Round [372] log likelihood: -5297.703951
EM: Round [373] log likelihood: -5297.703841
EM: Round [374] log likelihood: -5297.703733
EM: Round [375] log likelihood: -5297.703626
EM: Round [376] log likelihood: -5297.703520
EM: Round [377] log likelihood: -5297.703416
EM: Round [378] log likelihood: -5297.703313
EM: Round [379] log likelihood: -5297.703212
EM: Round [380] log likelihood: -5297.703111
EM: Round [381] log likelihood: -5297.703012
EM: Stopping iterations at round 381 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir
-done, see /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3717.800335
EM: Round [1] log likelihood: -3716.061491
EM: Round [2] log likelihood: -3716.061419
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295822882
Execution Time = 5.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.i1B8rRXG8j/fi_workdir/microH.dat
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.i1B8rRXG8j/fi_workdir/microH.dat /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_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.i1B8rRXG8j/fi_workdir/microH.dat /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.i1B8rRXG8j --json_outfile /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.i1B8rRXG8j --json_outfile /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000197585.10]
WARNING, no entry stored in dbm for [ENSG00000197585.10]
WARNING, no entry stored in dbm for [ENSG00000197585.10]
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 [ENSG00000272168.8]
WARNING, no entry stored in dbm for [ENSG00000272168.8]
WARNING, no entry stored in dbm for [ENSG00000272168.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.i1B8rRXG8j/ctat_genome_lib_build_dir > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.i1B8rRXG8j/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory