Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/2f93855d9aa2a18c4371fa0ddd78e7/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.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/68/c195ee4328eb5b350b2b58ec48cef6/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/67dbb04b02ece8475f8e9e69fea094/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/67dbb04b02ece8475f8e9e69fea094/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/2f93855d9aa2a18c4371fa0ddd78e7/659_wQ-T1-TRNA-1_B23MHV2LT4_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_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-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_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/cytoBand.txt
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.G4FK4Af86Y/fi_workdir --reads "/tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:07:21 ..... started STAR run
Jun 08 10:07:22 ..... loading genome
Jun 08 10:09:09 ... generating Suffix Array index
Jun 08 10:12:52 ... completed Suffix Array index
Jun 08 10:12:52 ..... processing annotations GTF
Jun 08 10:12:53 ..... inserting junctions into the genome indices
Jun 08 10:13:54 ..... started mapping
Jun 08 11:28:05 ..... finished mapping
Jun 08 11:28:07 ..... started sorting BAM
Jun 08 11:28:08 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 80.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.G4FK4Af86Y/fi_workdir --reads "/tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:28:17 : INFO : Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[1410000] -done parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 174,
'exons hit < 2' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'small anchor length' => 2,
'excessive soft clipping' => 9651,
'per_id < 96' => 5169,
'low complexity anchor region' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 16,
'seq-similar region overlap' => 387,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
' ** passed ** ' => 7264,
'num genes matched < 2' => 12
};
-writing fusion junction support info.
Execution Time = 0.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[32000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[23000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[24000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[40000] -fusion SPANNING read extraction for scaff: TRHDE--CYP27B1
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 66817,
'lacks exon overlap' => 16884
};
Execution Time = 1.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4385.554985
EM: Round [1] log likelihood: -4382.836654
EM: Round [2] log likelihood: -4382.122546
EM: Round [3] log likelihood: -4381.504305
EM: Round [4] log likelihood: -4380.962129
EM: Round [5] log likelihood: -4380.485415
EM: Round [6] log likelihood: -4380.065278
EM: Round [7] log likelihood: -4379.694209
EM: Round [8] log likelihood: -4379.365830
EM: Round [9] log likelihood: -4379.074697
EM: Round [10] log likelihood: -4378.816142
EM: Round [11] log likelihood: -4378.586153
EM: Round [12] log likelihood: -4378.381263
EM: Round [13] log likelihood: -4378.198473
EM: Round [14] log likelihood: -4378.035179
EM: Round [15] log likelihood: -4377.889113
EM: Round [16] log likelihood: -4377.758299
EM: Round [17] log likelihood: -4377.641007
EM: Round [18] log likelihood: -4377.535722
EM: Round [19] log likelihood: -4377.441114
EM: Round [20] log likelihood: -4377.356014
EM: Round [21] log likelihood: -4377.279391
EM: Round [22] log likelihood: -4377.210336
EM: Round [23] log likelihood: -4377.148046
EM: Round [24] log likelihood: -4377.091809
EM: Round [25] log likelihood: -4377.040997
EM: Round [26] log likelihood: -4376.995049
EM: Round [27] log likelihood: -4376.953468
EM: Round [28] log likelihood: -4376.915812
EM: Round [29] log likelihood: -4376.881687
EM: Round [30] log likelihood: -4376.850742
EM: Round [31] log likelihood: -4376.822662
EM: Round [32] log likelihood: -4376.797166
EM: Round [33] log likelihood: -4376.774004
EM: Round [34] log likelihood: -4376.752951
EM: Round [35] log likelihood: -4376.733803
EM: Round [36] log likelihood: -4376.716381
EM: Round [37] log likelihood: -4376.700521
EM: Round [38] log likelihood: -4376.686076
EM: Round [39] log likelihood: -4376.672914
EM: Round [40] log likelihood: -4376.660917
EM: Round [41] log likelihood: -4376.649978
EM: Round [42] log likelihood: -4376.639998
EM: Round [43] log likelihood: -4376.630892
EM: Round [44] log likelihood: -4376.622579
EM: Round [45] log likelihood: -4376.614988
EM: Round [46] log likelihood: -4376.608055
EM: Round [47] log likelihood: -4376.601720
EM: Round [48] log likelihood: -4376.595931
EM: Round [49] log likelihood: -4376.590638
EM: Round [50] log likelihood: -4376.585799
EM: Round [51] log likelihood: -4376.581373
EM: Round [52] log likelihood: -4376.577325
EM: Round [53] log likelihood: -4376.573620
EM: Round [54] log likelihood: -4376.570230
EM: Round [55] log likelihood: -4376.567127
EM: Round [56] log likelihood: -4376.564287
EM: Round [57] log likelihood: -4376.561686
EM: Round [58] log likelihood: -4376.559304
EM: Round [59] log likelihood: -4376.557123
EM: Round [60] log likelihood: -4376.555124
EM: Round [61] log likelihood: -4376.553294
EM: Round [62] log likelihood: -4376.551616
EM: Round [63] log likelihood: -4376.550079
EM: Round [64] log likelihood: -4376.548671
EM: Round [65] log likelihood: -4376.547380
EM: Round [66] log likelihood: -4376.546196
EM: Round [67] log likelihood: -4376.545111
EM: Round [68] log likelihood: -4376.544117
EM: Round [69] log likelihood: -4376.543205
EM: Round [70] log likelihood: -4376.542369
EM: Round [71] log likelihood: -4376.541602
EM: Round [72] log likelihood: -4376.540899
EM: Round [73] log likelihood: -4376.540254
EM: Round [74] log likelihood: -4376.539662
EM: Round [75] log likelihood: -4376.539119
EM: Round [76] log likelihood: -4376.538622
EM: Round [77] log likelihood: -4376.538165
EM: Round [78] log likelihood: -4376.537746
EM: Round [79] log likelihood: -4376.537362
EM: Round [80] log likelihood: -4376.537009
EM: Round [81] log likelihood: -4376.536686
EM: Round [82] log likelihood: -4376.536389
EM: Round [83] log likelihood: -4376.536117
EM: Round [84] log likelihood: -4376.535867
EM: Round [85] log likelihood: -4376.535637
EM: Round [86] log likelihood: -4376.535427
EM: Round [87] log likelihood: -4376.535234
EM: Round [88] log likelihood: -4376.535057
EM: Round [89] log likelihood: -4376.534894
EM: Round [90] log likelihood: -4376.534745
EM: Round [91] log likelihood: -4376.534608
EM: Round [92] log likelihood: -4376.534482
EM: Round [93] log likelihood: -4376.534367
EM: Round [94] log likelihood: -4376.534261
EM: Round [95] log likelihood: -4376.534163
EM: Stopping iterations at round 95 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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir
-done, see /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3842.033512
EM: Round [1] log likelihood: -3841.500271
EM: Round [2] log likelihood: -3841.498032
EM: Round [3] log likelihood: -3841.498010
EM: Stopping iterations at round 3 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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295130272
Execution Time = 5.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/fi_workdir/microH.dat
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.G4FK4Af86Y/fi_workdir/microH.dat /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/microH.dat /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.G4FK4Af86Y --json_outfile /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_wQ-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.G4FK4Af86Y --json_outfile /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [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 [ENSG00000288546.1]
WARNING, no entry stored in dbm for [ENSG00000288546.1]
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 [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory