Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/a213f810f00095d3a0265ae99a4592/tih_rna_sample_00146_B23WHTKLT4_2.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/44/3c2709c7c4bb69b4d4c39d04e69a31/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/ed8c2d0ed711b1d1fe9b92a4441571/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/ed8c2d0ed711b1d1fe9b92a4441571/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/3c2709c7c4bb69b4d4c39d04e69a31/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00146_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2 --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 tih_rna_sample_00146_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/cytoBand.txt
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00146_B23WHTKLT4_2.star --out_dir /tmp/nxf.mozZzLS8CN/fi_workdir --reads "/tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:08:43 ..... started STAR run
Jun 08 10:08:43 ..... loading genome
Jun 08 10:10:41 ... generating Suffix Array index
Jun 08 10:14:56 ... completed Suffix Array index
Jun 08 10:14:56 ..... processing annotations GTF
Jun 08 10:14:57 ..... inserting junctions into the genome indices
Jun 08 10:16:07 ..... started mapping
Jun 08 11:43:17 ..... finished mapping
Jun 08 11:43:20 ..... started sorting BAM
Jun 08 11:43:21 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 94.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00146_B23WHTKLT4_2.star --out_dir /tmp/nxf.mozZzLS8CN/fi_workdir --reads "/tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --remove_dups
11:43:27 : INFO : Done.
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
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[900000] -done parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
' ** passed ** ' => 8209,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
'per_id < 96' => 3268,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 82,
'excessive soft clipping' => 11193,
'exons hit < 2' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 92,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 613,
'small anchor length' => 29,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 958,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1846,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'low complexity anchor region' => 13,
'num genes matched < 2' => 51
};
-writing fusion junction support info.
Execution Time = 0.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[43000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[119000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[23000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[8000] -fusion SPANNING read extraction for scaff: UPK3B--AC211486.3
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[136000] -fusion SPANNING read extraction for scaff: ZFHX3--LINC01572
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 28464,
'seq similar region alignment' => 18606
};
Execution Time = 1.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6205.277206
EM: Round [1] log likelihood: -6200.753596
EM: Round [2] log likelihood: -6200.724714
EM: Round [3] log likelihood: -6200.715455
EM: Round [4] log likelihood: -6200.706321
EM: Round [5] log likelihood: -6200.697273
EM: Round [6] log likelihood: -6200.688309
EM: Round [7] log likelihood: -6200.679428
EM: Round [8] log likelihood: -6200.670630
EM: Round [9] log likelihood: -6200.661912
EM: Round [10] log likelihood: -6200.653275
EM: Round [11] log likelihood: -6200.644718
EM: Round [12] log likelihood: -6200.636238
EM: Round [13] log likelihood: -6200.627837
EM: Round [14] log likelihood: -6200.619511
EM: Round [15] log likelihood: -6200.611262
EM: Round [16] log likelihood: -6200.603087
EM: Round [17] log likelihood: -6200.594985
EM: Round [18] log likelihood: -6200.586957
EM: Round [19] log likelihood: -6200.579001
EM: Round [20] log likelihood: -6200.571116
EM: Round [21] log likelihood: -6200.563302
EM: Round [22] log likelihood: -6200.555557
EM: Round [23] log likelihood: -6200.547881
EM: Round [24] log likelihood: -6200.540273
EM: Round [25] log likelihood: -6200.532733
EM: Round [26] log likelihood: -6200.525259
EM: Round [27] log likelihood: -6200.517851
EM: Round [28] log likelihood: -6200.510507
EM: Round [29] log likelihood: -6200.503229
EM: Round [30] log likelihood: -6200.496013
EM: Round [31] log likelihood: -6200.488861
EM: Round [32] log likelihood: -6200.481771
EM: Round [33] log likelihood: -6200.474742
EM: Round [34] log likelihood: -6200.467774
EM: Round [35] log likelihood: -6200.460866
EM: Round [36] log likelihood: -6200.454018
EM: Round [37] log likelihood: -6200.447228
EM: Round [38] log likelihood: -6200.440497
EM: Round [39] log likelihood: -6200.433824
EM: Round [40] log likelihood: -6200.427207
EM: Round [41] log likelihood: -6200.420647
EM: Round [42] log likelihood: -6200.414142
EM: Round [43] log likelihood: -6200.407693
EM: Round [44] log likelihood: -6200.401298
EM: Round [45] log likelihood: -6200.394957
EM: Round [46] log likelihood: -6200.388670
EM: Round [47] log likelihood: -6200.382436
EM: Round [48] log likelihood: -6200.376253
EM: Round [49] log likelihood: -6200.370123
EM: Round [50] log likelihood: -6200.364044
EM: Round [51] log likelihood: -6200.358015
EM: Round [52] log likelihood: -6200.352037
EM: Round [53] log likelihood: -6200.346109
EM: Round [54] log likelihood: -6200.340229
EM: Round [55] log likelihood: -6200.334398
EM: Round [56] log likelihood: -6200.328616
EM: Round [57] log likelihood: -6200.322881
EM: Round [58] log likelihood: -6200.317193
EM: Round [59] log likelihood: -6200.311552
EM: Round [60] log likelihood: -6200.305957
EM: Round [61] log likelihood: -6200.300408
EM: Round [62] log likelihood: -6200.294904
EM: Round [63] log likelihood: -6200.289445
EM: Round [64] log likelihood: -6200.284031
EM: Round [65] log likelihood: -6200.278660
EM: Round [66] log likelihood: -6200.273333
EM: Round [67] log likelihood: -6200.268049
EM: Round [68] log likelihood: -6200.262808
EM: Round [69] log likelihood: -6200.257609
EM: Round [70] log likelihood: -6200.252452
EM: Round [71] log likelihood: -6200.247336
EM: Round [72] log likelihood: -6200.242262
EM: Round [73] log likelihood: -6200.237228
EM: Round [74] log likelihood: -6200.232234
EM: Round [75] log likelihood: -6200.227280
EM: Round [76] log likelihood: -6200.222366
EM: Round [77] log likelihood: -6200.217490
EM: Round [78] log likelihood: -6200.212654
EM: Round [79] log likelihood: -6200.207856
EM: Round [80] log likelihood: -6200.203096
EM: Round [81] log likelihood: -6200.198373
EM: Round [82] log likelihood: -6200.193688
EM: Round [83] log likelihood: -6200.189039
EM: Round [84] log likelihood: -6200.184427
EM: Round [85] log likelihood: -6200.179852
EM: Round [86] log likelihood: -6200.175312
EM: Round [87] log likelihood: -6200.170808
EM: Round [88] log likelihood: -6200.166339
EM: Round [89] log likelihood: -6200.161905
EM: Round [90] log likelihood: -6200.157506
EM: Round [91] log likelihood: -6200.153141
EM: Round [92] log likelihood: -6200.148809
EM: Round [93] log likelihood: -6200.144512
EM: Round [94] log likelihood: -6200.140247
EM: Round [95] log likelihood: -6200.136016
EM: Round [96] log likelihood: -6200.131818
EM: Round [97] log likelihood: -6200.127652
EM: Round [98] log likelihood: -6200.123517
EM: Round [99] log likelihood: -6200.119415
EM: Round [100] log likelihood: -6200.115345
EM: Round [101] log likelihood: -6200.111305
EM: Round [102] log likelihood: -6200.107297
EM: Round [103] log likelihood: -6200.103319
EM: Round [104] log likelihood: -6200.099372
EM: Round [105] log likelihood: -6200.095454
EM: Round [106] log likelihood: -6200.091567
EM: Round [107] log likelihood: -6200.087709
EM: Round [108] log likelihood: -6200.083881
EM: Round [109] log likelihood: -6200.080082
EM: Round [110] log likelihood: -6200.076311
EM: Round [111] log likelihood: -6200.072569
EM: Round [112] log likelihood: -6200.068856
EM: Round [113] log likelihood: -6200.065170
EM: Round [114] log likelihood: -6200.061513
EM: Round [115] log likelihood: -6200.057883
EM: Round [116] log likelihood: -6200.054280
EM: Round [117] log likelihood: -6200.050704
EM: Round [118] log likelihood: -6200.047156
EM: Round [119] log likelihood: -6200.043634
EM: Round [120] log likelihood: -6200.040138
EM: Round [121] log likelihood: -6200.036668
EM: Round [122] log likelihood: -6200.033225
EM: Round [123] log likelihood: -6200.029807
EM: Round [124] log likelihood: -6200.026414
EM: Round [125] log likelihood: -6200.023047
EM: Round [126] log likelihood: -6200.019705
EM: Round [127] log likelihood: -6200.016388
EM: Round [128] log likelihood: -6200.013096
EM: Round [129] log likelihood: -6200.009828
EM: Round [130] log likelihood: -6200.006584
EM: Round [131] log likelihood: -6200.003364
EM: Round [132] log likelihood: -6200.000168
EM: Round [133] log likelihood: -6199.996995
EM: Round [134] log likelihood: -6199.993846
EM: Round [135] log likelihood: -6199.990721
EM: Round [136] log likelihood: -6199.987618
EM: Round [137] log likelihood: -6199.984538
EM: Round [138] log likelihood: -6199.981481
EM: Round [139] log likelihood: -6199.978446
EM: Round [140] log likelihood: -6199.975433
EM: Round [141] log likelihood: -6199.972443
EM: Round [142] log likelihood: -6199.969474
EM: Round [143] log likelihood: -6199.966527
EM: Round [144] log likelihood: -6199.963602
EM: Round [145] log likelihood: -6199.960698
EM: Round [146] log likelihood: -6199.957815
EM: Round [147] log likelihood: -6199.954953
EM: Round [148] log likelihood: -6199.952112
EM: Round [149] log likelihood: -6199.949292
EM: Round [150] log likelihood: -6199.946492
EM: Round [151] log likelihood: -6199.943712
EM: Round [152] log likelihood: -6199.940953
EM: Round [153] log likelihood: -6199.938213
EM: Round [154] log likelihood: -6199.935494
EM: Round [155] log likelihood: -6199.932794
EM: Round [156] log likelihood: -6199.930114
EM: Round [157] log likelihood: -6199.927452
EM: Round [158] log likelihood: -6199.924811
EM: Round [159] log likelihood: -6199.922188
EM: Round [160] log likelihood: -6199.919584
EM: Round [161] log likelihood: -6199.916999
EM: Round [162] log likelihood: -6199.914432
EM: Round [163] log likelihood: -6199.911884
EM: Round [164] log likelihood: -6199.909354
EM: Round [165] log likelihood: -6199.906842
EM: Round [166] log likelihood: -6199.904348
EM: Round [167] log likelihood: -6199.901872
EM: Round [168] log likelihood: -6199.899414
EM: Round [169] log likelihood: -6199.896973
EM: Round [170] log likelihood: -6199.894550
EM: Round [171] log likelihood: -6199.892144
EM: Round [172] log likelihood: -6199.889755
EM: Round [173] log likelihood: -6199.887383
EM: Round [174] log likelihood: -6199.885028
EM: Round [175] log likelihood: -6199.882690
EM: Round [176] log likelihood: -6199.880368
EM: Round [177] log likelihood: -6199.878063
EM: Round [178] log likelihood: -6199.875775
EM: Round [179] log likelihood: -6199.873502
EM: Round [180] log likelihood: -6199.871246
EM: Round [181] log likelihood: -6199.869005
EM: Round [182] log likelihood: -6199.866780
EM: Round [183] log likelihood: -6199.864572
EM: Round [184] log likelihood: -6199.862378
EM: Round [185] log likelihood: -6199.860200
EM: Round [186] log likelihood: -6199.858038
EM: Round [187] log likelihood: -6199.855891
EM: Round [188] log likelihood: -6199.853759
EM: Round [189] log likelihood: -6199.851641
EM: Round [190] log likelihood: -6199.849539
EM: Round [191] log likelihood: -6199.847452
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EM: Round [651] log likelihood: -6199.552511
EM: Round [652] log likelihood: -6199.552409
EM: Round [653] log likelihood: -6199.552309
EM: Round [654] log likelihood: -6199.552209
EM: Round [655] log likelihood: -6199.552109
EM: Stopping iterations at round 655 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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/tih_rna_sample_00146_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa > /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2 --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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir
-done, see /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5147.304091
EM: Round [1] log likelihood: -5145.617989
EM: Round [2] log likelihood: -5145.615491
EM: Round [3] log likelihood: -5145.615485
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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz: 296087706
Execution Time = 6.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa --gtf /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fa --gtf /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf > /tmp/nxf.mozZzLS8CN/fi_workdir/microH.dat
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.mozZzLS8CN/fi_workdir/microH.dat /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/microH.dat /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.mozZzLS8CN --json_outfile /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00146_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.mozZzLS8CN --json_outfile /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00146_B23WHTKLT4_2
Running: touch /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00146_B23WHTKLT4_2 --html_output /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00146_B23WHTKLT4_2 --html_output /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.mozZzLS8CN/ctat_genome_lib_build_dir > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.mozZzLS8CN/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory