Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/d92823920bab052015b7764e88816d/tih_rna_sample_00760_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/3c07a917ae369e3cc208affded456d/tih_rna_sample_00760_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/db06508b6252a3f9d4a4bec5b2eb2a/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/db06508b6252a3f9d4a4bec5b2eb2a/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/d92823920bab052015b7764e88816d/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00760_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00760_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/cytoBand.txt
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00760_B23MVV7LT4_1.star --out_dir /tmp/nxf.bkEML7IVg5/fi_workdir --reads "/tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:54:05 ..... started STAR run
Jun 08 09:54:05 ..... loading genome
Jun 08 09:55:50 ... generating Suffix Array index
Jun 08 09:59:40 ... completed Suffix Array index
Jun 08 09:59:40 ..... processing annotations GTF
Jun 08 09:59:40 ..... inserting junctions into the genome indices
Jun 08 10:00:41 ..... started mapping
Jun 08 10:53:16 ..... finished mapping
Jun 08 10:53:18 ..... started sorting BAM
Jun 08 10:53:18 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 59.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00760_B23MVV7LT4_1.star --out_dir /tmp/nxf.bkEML7IVg5/fi_workdir --reads "/tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:53:20 : INFO : Done.
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[280000] -done parsing /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 1,
'low complexity anchor region' => 40,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14,
'per_id < 96' => 1167,
'exons hit < 2' => 1,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 61,
' ** passed ** ' => 45445,
'excessive soft clipping' => 1853,
'seq-similar region overlap' => 56,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 52,
'small anchor length' => 212
};
-writing fusion junction support info.
Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 429,
'seq similar region alignment' => 15567
};
Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2001.551866
EM: Round [1] log likelihood: -2001.443877
EM: Round [2] log likelihood: -2001.422332
EM: Round [3] log likelihood: -2001.402281
EM: Round [4] log likelihood: -2001.383474
EM: Round [5] log likelihood: -2001.365809
EM: Round [6] log likelihood: -2001.349195
EM: Round [7] log likelihood: -2001.333551
EM: Round [8] log likelihood: -2001.318805
EM: Round [9] log likelihood: -2001.304892
EM: Round [10] log likelihood: -2001.291750
EM: Round [11] log likelihood: -2001.279326
EM: Round [12] log likelihood: -2001.267570
EM: Round [13] log likelihood: -2001.256437
EM: Round [14] log likelihood: -2001.245885
EM: Round [15] log likelihood: -2001.235876
EM: Round [16] log likelihood: -2001.226376
EM: Round [17] log likelihood: -2001.217351
EM: Round [18] log likelihood: -2001.208772
EM: Round [19] log likelihood: -2001.200612
EM: Round [20] log likelihood: -2001.192845
EM: Round [21] log likelihood: -2001.185446
EM: Round [22] log likelihood: -2001.178395
EM: Round [23] log likelihood: -2001.171671
EM: Round [24] log likelihood: -2001.165254
EM: Round [25] log likelihood: -2001.159127
EM: Round [26] log likelihood: -2001.153274
EM: Round [27] log likelihood: -2001.147678
EM: Round [28] log likelihood: -2001.142326
EM: Round [29] log likelihood: -2001.137204
EM: Round [30] log likelihood: -2001.132299
EM: Round [31] log likelihood: -2001.127599
EM: Round [32] log likelihood: -2001.123093
EM: Round [33] log likelihood: -2001.118770
EM: Round [34] log likelihood: -2001.114622
EM: Round [35] log likelihood: -2001.110638
EM: Round [36] log likelihood: -2001.106810
EM: Round [37] log likelihood: -2001.103129
EM: Round [38] log likelihood: -2001.099588
EM: Round [39] log likelihood: -2001.096180
EM: Round [40] log likelihood: -2001.092897
EM: Round [41] log likelihood: -2001.089734
EM: Round [42] log likelihood: -2001.086684
EM: Round [43] log likelihood: -2001.083741
EM: Round [44] log likelihood: -2001.080900
EM: Round [45] log likelihood: -2001.078156
EM: Round [46] log likelihood: -2001.075504
EM: Round [47] log likelihood: -2001.072939
EM: Round [48] log likelihood: -2001.070456
EM: Round [49] log likelihood: -2001.068053
EM: Round [50] log likelihood: -2001.065725
EM: Round [51] log likelihood: -2001.063467
EM: Round [52] log likelihood: -2001.061278
EM: Round [53] log likelihood: -2001.059152
EM: Round [54] log likelihood: -2001.057088
EM: Round [55] log likelihood: -2001.055082
EM: Round [56] log likelihood: -2001.053132
EM: Round [57] log likelihood: -2001.051234
EM: Round [58] log likelihood: -2001.049387
EM: Round [59] log likelihood: -2001.047587
EM: Round [60] log likelihood: -2001.045833
EM: Round [61] log likelihood: -2001.044122
EM: Round [62] log likelihood: -2001.042452
EM: Round [63] log likelihood: -2001.040821
EM: Round [64] log likelihood: -2001.039228
EM: Round [65] log likelihood: -2001.037671
EM: Round [66] log likelihood: -2001.036147
EM: Round [67] log likelihood: -2001.034656
EM: Round [68] log likelihood: -2001.033196
EM: Round [69] log likelihood: -2001.031766
EM: Round [70] log likelihood: -2001.030363
EM: Round [71] log likelihood: -2001.028987
EM: Round [72] log likelihood: -2001.027637
EM: Round [73] log likelihood: -2001.026311
EM: Round [74] log likelihood: -2001.025008
EM: Round [75] log likelihood: -2001.023727
EM: Round [76] log likelihood: -2001.022468
EM: Round [77] log likelihood: -2001.021229
EM: Round [78] log likelihood: -2001.020009
EM: Round [79] log likelihood: -2001.018807
EM: Round [80] log likelihood: -2001.017623
EM: Round [81] log likelihood: -2001.016456
EM: Round [82] log likelihood: -2001.015305
EM: Round [83] log likelihood: -2001.014170
EM: Round [84] log likelihood: -2001.013049
EM: Round [85] log likelihood: -2001.011942
EM: Round [86] log likelihood: -2001.010849
EM: Round [87] log likelihood: -2001.009768
EM: Round [88] log likelihood: -2001.008700
EM: Round [89] log likelihood: -2001.007643
EM: Round [90] log likelihood: -2001.006598
EM: Round [91] log likelihood: -2001.005564
EM: Round [92] log likelihood: -2001.004539
EM: Round [93] log likelihood: -2001.003525
EM: Round [94] log likelihood: -2001.002520
EM: Round [95] log likelihood: -2001.001525
EM: Round [96] log likelihood: -2001.000538
EM: Round [97] log likelihood: -2000.999559
EM: Round [98] log likelihood: -2000.998589
EM: Round [99] log likelihood: -2000.997626
EM: Round [100] log likelihood: -2000.996670
EM: Round [101] log likelihood: -2000.995722
EM: Round [102] log likelihood: -2000.994780
EM: Round [103] log likelihood: -2000.993845
EM: Round [104] log likelihood: -2000.992916
EM: Round [105] log likelihood: -2000.991994
EM: Round [106] log likelihood: -2000.991077
EM: Round [107] log likelihood: -2000.990166
EM: Round [108] log likelihood: -2000.989260
EM: Round [109] log likelihood: -2000.988359
EM: Round [110] log likelihood: -2000.987464
EM: Round [111] log likelihood: -2000.986573
EM: Round [112] log likelihood: -2000.985687
EM: Round [113] log likelihood: -2000.984805
EM: Round [114] log likelihood: -2000.983928
EM: Round [115] log likelihood: -2000.983055
EM: Round [116] log likelihood: -2000.982186
EM: Round [117] log likelihood: -2000.981321
EM: Round [118] log likelihood: -2000.980460
EM: Round [119] log likelihood: -2000.979602
EM: Round [120] log likelihood: -2000.978748
EM: Round [121] log likelihood: -2000.977898
EM: Round [122] log likelihood: -2000.977050
EM: Round [123] log likelihood: -2000.976206
EM: Round [124] log likelihood: -2000.975365
EM: Round [125] log likelihood: -2000.974528
EM: Round [126] log likelihood: -2000.973693
EM: Round [127] log likelihood: -2000.972861
EM: Round [128] log likelihood: -2000.972032
EM: Round [129] log likelihood: -2000.971205
EM: Round [130] log likelihood: -2000.970381
EM: Round [131] log likelihood: -2000.969560
EM: Round [132] log likelihood: -2000.968741
EM: Round [133] log likelihood: -2000.967925
EM: Round [134] log likelihood: -2000.967111
EM: Round [135] log likelihood: -2000.966300
EM: Round [136] log likelihood: -2000.965490
EM: Round [137] log likelihood: -2000.964683
EM: Round [138] log likelihood: -2000.963879
EM: Round [139] log likelihood: -2000.963076
EM: Round [140] log likelihood: -2000.962275
EM: Round [141] log likelihood: -2000.961477
EM: Round [142] log likelihood: -2000.960680
EM: Round [143] log likelihood: -2000.959886
EM: Round [144] log likelihood: -2000.959093
EM: Round [145] log likelihood: -2000.958302
EM: Round [146] log likelihood: -2000.957513
EM: Round [147] log likelihood: -2000.956726
EM: Round [148] log likelihood: -2000.955941
EM: Round [149] log likelihood: -2000.955157
EM: Round [150] log likelihood: -2000.954375
EM: Round [151] log likelihood: -2000.953595
EM: Round [152] log likelihood: -2000.952817
EM: Round [153] log likelihood: -2000.952040
EM: Round [154] log likelihood: -2000.951265
EM: Round [155] log likelihood: -2000.950492
EM: Round [156] log likelihood: -2000.949720
EM: Round [157] log likelihood: -2000.948949
EM: Round [158] log likelihood: -2000.948180
EM: Round [159] log likelihood: -2000.947413
EM: Round [160] log likelihood: -2000.946647
EM: Round [161] log likelihood: -2000.945883
EM: Round [162] log likelihood: -2000.945120
EM: Round [163] log likelihood: -2000.944359
EM: Round [164] log likelihood: -2000.943599
EM: Round [165] log likelihood: -2000.942841
EM: Round [166] log likelihood: -2000.942084
EM: Round [167] log likelihood: -2000.941328
EM: Round [168] log likelihood: -2000.940574
EM: Round [169] log likelihood: -2000.939821
EM: Round [170] log likelihood: -2000.939069
EM: Round [171] log likelihood: -2000.938319
EM: Round [172] log likelihood: -2000.937570
EM: Round [173] log likelihood: -2000.936823
EM: Round [174] log likelihood: -2000.936076
EM: Round [175] log likelihood: -2000.935332
EM: Round [176] log likelihood: -2000.934588
EM: Round [177] log likelihood: -2000.933846
EM: Round [178] log likelihood: -2000.933105
EM: Round [179] log likelihood: -2000.932365
EM: Round [180] log likelihood: -2000.931627
EM: Round [181] log likelihood: -2000.930889
EM: Round [182] log likelihood: -2000.930153
EM: Round [183] log likelihood: -2000.929419
EM: Round [184] log likelihood: -2000.928685
EM: Round [185] log likelihood: -2000.927953
EM: Round [186] log likelihood: -2000.927222
EM: Round [187] log likelihood: -2000.926492
EM: Round [188] log likelihood: -2000.925764
EM: Round [189] log likelihood: -2000.925036
EM: Round [190] log likelihood: -2000.924310
EM: Round [191] log likelihood: -2000.923585
EM: Round [192] log likelihood: -2000.922861
EM: Round [193] log likelihood: -2000.922138
EM: Round [194] log likelihood: -2000.921417
EM: Round [195] log likelihood: -2000.920697
EM: Round [196] log likelihood: -2000.919978
EM: Round [197] log likelihood: -2000.919260
EM: Round [198] log likelihood: -2000.918543
EM: Round [199] log likelihood: -2000.917827
EM: Round [200] log likelihood: -2000.917113
EM: Round [201] log likelihood: -2000.916399
EM: Round [202] log likelihood: -2000.915687
EM: Round [203] log likelihood: -2000.914976
EM: Round [204] log likelihood: -2000.914266
EM: Round [205] log likelihood: -2000.913557
EM: Round [206] log likelihood: -2000.912850
EM: Round [207] log likelihood: -2000.912143
EM: Round [208] log likelihood: -2000.911438
EM: Round [209] log likelihood: -2000.910734
EM: Round [210] log likelihood: -2000.910030
EM: Round [211] log likelihood: -2000.909328
EM: Round [212] log likelihood: -2000.908627
EM: Round [213] log likelihood: -2000.907927
EM: Round [214] log likelihood: -2000.907229
EM: Round [215] log likelihood: -2000.906531
EM: Round [216] log likelihood: -2000.905834
EM: Round [217] log likelihood: -2000.905139
EM: Round [218] log likelihood: -2000.904444
EM: Round [219] log likelihood: -2000.903751
EM: Round [220] log likelihood: -2000.903059
EM: Round [221] log likelihood: -2000.902368
EM: Round [222] log likelihood: -2000.901678
EM: Round [223] log likelihood: -2000.900989
EM: Round [224] log likelihood: -2000.900301
EM: Round [225] log likelihood: -2000.899614
EM: Round [226] log likelihood: -2000.898928
EM: Round [227] log likelihood: -2000.898243
EM: Round [228] log likelihood: -2000.897560
EM: Round [229] log likelihood: -2000.896877
EM: Round [230] log likelihood: -2000.896196
EM: Round [231] log likelihood: -2000.895515
EM: Round [232] log likelihood: -2000.894836
EM: Round [233] log likelihood: -2000.894157
EM: Round [234] log likelihood: -2000.893480
EM: Round [235] log likelihood: -2000.892804
EM: Round [236] log likelihood: -2000.892128
EM: Round [237] log likelihood: -2000.891454
EM: Round [238] log likelihood: -2000.890781
EM: Round [239] log likelihood: -2000.890109
EM: Round [240] log likelihood: -2000.889438
EM: Round [241] log likelihood: -2000.888768
EM: Round [242] log likelihood: -2000.888099
EM: Round [243] log likelihood: -2000.887431
EM: Round [244] log likelihood: -2000.886764
EM: Round [245] log likelihood: -2000.886098
EM: Round [246] log likelihood: -2000.885433
EM: Round [247] log likelihood: -2000.884769
EM: Round [248] log likelihood: -2000.884106
EM: Round [249] log likelihood: -2000.883444
EM: Round [250] log likelihood: -2000.882783
EM: Round [251] log likelihood: -2000.882123
EM: Round [252] log likelihood: -2000.881464
EM: Round [253] log likelihood: -2000.880807
EM: Round [254] log likelihood: -2000.880150
EM: Round [255] log likelihood: -2000.879494
EM: Round [256] log likelihood: -2000.878839
EM: Round [257] log likelihood: -2000.878185
EM: Round [258] log likelihood: -2000.877533
EM: Round [259] log likelihood: -2000.876881
EM: Round [260] log likelihood: -2000.876230
EM: Round [261] log likelihood: -2000.875580
EM: Round [262] log likelihood: -2000.874931
EM: Round [263] log likelihood: -2000.874283
EM: Round [264] log likelihood: -2000.873637
EM: Round [265] log likelihood: -2000.872991
EM: Round [266] log likelihood: -2000.872346
EM: Round [267] log likelihood: -2000.871702
EM: Round [268] log likelihood: -2000.871059
EM: Round [269] log likelihood: -2000.870417
EM: Round [270] log likelihood: -2000.869776
EM: Round [271] log likelihood: -2000.869136
EM: Round [272] log likelihood: -2000.868497
EM: Round [273] log likelihood: -2000.867859
EM: Round [274] log likelihood: -2000.867222
EM: Round [275] log likelihood: -2000.866586
EM: Round [276] log likelihood: -2000.865951
EM: Round [277] log likelihood: -2000.865317
EM: Round [278] log likelihood: -2000.864683
EM: Round [279] log likelihood: -2000.864051
EM: Round [280] log likelihood: -2000.863420
EM: Round [281] log likelihood: -2000.862789
EM: Round [282] log likelihood: -2000.862160
EM: Round [283] log likelihood: -2000.861532
EM: Round [284] log likelihood: -2000.860904
EM: Round [285] log likelihood: -2000.860278
EM: Round [286] log likelihood: -2000.859652
EM: Round [287] log likelihood: -2000.859028
EM: Round [288] log likelihood: -2000.858404
EM: Round [289] log likelihood: -2000.857781
EM: Round [290] log likelihood: -2000.857159
EM: Round [291] log likelihood: -2000.856539
EM: Round [292] log likelihood: -2000.855919
EM: Round [293] log likelihood: -2000.855300
EM: Round [294] log likelihood: -2000.854682
EM: Round [295] log likelihood: -2000.854065
EM: Round [296] log likelihood: -2000.853448
EM: Round [297] log likelihood: -2000.852833
EM: Round [298] log likelihood: -2000.852219
EM: Round [299] log likelihood: -2000.851606
EM: Round [300] log likelihood: -2000.850993
EM: Round [301] log likelihood: -2000.850382
EM: Round [302] log likelihood: -2000.849771
EM: Round [303] log likelihood: -2000.849161
EM: Round [304] log likelihood: -2000.848553
EM: Round [305] log likelihood: -2000.847945
EM: Round [306] log likelihood: -2000.847338
EM: Round [307] log likelihood: -2000.846732
EM: Round [308] log likelihood: -2000.846127
EM: Round [309] log likelihood: -2000.845523
EM: Round [310] log likelihood: -2000.844920
EM: Round [311] log likelihood: -2000.844317
EM: Round [312] log likelihood: -2000.843716
EM: Round [313] log likelihood: -2000.843115
EM: Round [314] log likelihood: -2000.842516
EM: Round [315] log likelihood: -2000.841917
EM: Round [316] log likelihood: -2000.841319
EM: Round [317] log likelihood: -2000.840722
EM: Round [318] log likelihood: -2000.840126
EM: Round [319] log likelihood: -2000.839531
EM: Round [320] log likelihood: -2000.838937
EM: Round [321] log likelihood: -2000.838344
EM: Round [322] log likelihood: -2000.837751
EM: Round [323] log likelihood: -2000.837160
EM: Round [324] log likelihood: -2000.836569
EM: Round [325] log likelihood: -2000.835979
EM: Round [326] log likelihood: -2000.835390
EM: Round [327] log likelihood: -2000.834802
EM: Round [328] log likelihood: -2000.834215
EM: Round [329] log likelihood: -2000.833629
EM: Round [330] log likelihood: -2000.833044
EM: Round [331] log likelihood: -2000.832459
EM: Round [332] log likelihood: -2000.831876
EM: Round [333] log likelihood: -2000.831293
EM: Round [334] log likelihood: -2000.830711
EM: Round [335] log likelihood: -2000.830130
EM: Round [336] log likelihood: -2000.829550
EM: Round [337] log likelihood: -2000.828971
EM: Round [338] log likelihood: -2000.828393
EM: Round [339] log likelihood: -2000.827815
EM: Round [340] log likelihood: -2000.827238
EM: Round [341] log likelihood: -2000.826663
EM: Round [342] log likelihood: -2000.826088
EM: Round [343] log likelihood: -2000.825514
EM: Round [344] log likelihood: -2000.824941
EM: Round [345] log likelihood: -2000.824368
EM: Round [346] log likelihood: -2000.823797
EM: Round [347] log likelihood: -2000.823226
EM: Round [348] log likelihood: -2000.822656
EM: Round [349] log likelihood: -2000.822088
EM: Round [350] log likelihood: -2000.821520
EM: Round [351] log likelihood: -2000.820952
EM: Round [352] log likelihood: -2000.820386
EM: Round [353] log likelihood: -2000.819821
EM: Round [354] log likelihood: -2000.819256
EM: Round [355] log likelihood: -2000.818692
EM: Round [356] log likelihood: -2000.818129
EM: Round [357] log likelihood: -2000.817567
EM: Round [358] log likelihood: -2000.817006
EM: Round [359] log likelihood: -2000.816445
EM: Round [360] log likelihood: -2000.815886
EM: Round [361] log likelihood: -2000.815327
EM: Round [362] log likelihood: -2000.814769
EM: Round [363] log likelihood: -2000.814212
EM: Round [364] log likelihood: -2000.813656
EM: Round [365] log likelihood: -2000.813100
EM: Round [366] log likelihood: -2000.812546
EM: Round [367] log likelihood: -2000.811992
EM: Round [368] log likelihood: -2000.811439
EM: Round [369] log likelihood: -2000.810887
EM: Round [370] log likelihood: -2000.810335
EM: Round [371] log likelihood: -2000.809785
EM: Round [372] log likelihood: -2000.809235
EM: Round [373] log likelihood: -2000.808686
EM: Round [374] log likelihood: -2000.808138
EM: Round [375] log likelihood: -2000.807591
EM: Round [376] log likelihood: -2000.807045
EM: Round [377] log likelihood: -2000.806499
EM: Round [378] log likelihood: -2000.805954
EM: Round [379] log likelihood: -2000.805410
EM: Round [380] log likelihood: -2000.804867
EM: Round [381] log likelihood: -2000.804325
EM: Round [382] log likelihood: -2000.803783
EM: Round [383] log likelihood: -2000.803243
EM: Round [384] log likelihood: -2000.802703
EM: Round [385] log likelihood: -2000.802164
EM: Round [386] log likelihood: -2000.801625
EM: Round [387] log likelihood: -2000.801088
EM: Round [388] log likelihood: -2000.800551
EM: Round [389] log likelihood: -2000.800015
EM: Round [390] log likelihood: -2000.799480
EM: Round [391] log likelihood: -2000.798946
EM: Round [392] log likelihood: -2000.798412
EM: Round [393] log likelihood: -2000.797879
EM: Round [394] log likelihood: -2000.797347
EM: Round [395] log likelihood: -2000.796816
EM: Round [396] log likelihood: -2000.796286
EM: Round [397] log likelihood: -2000.795756
EM: Round [398] log likelihood: -2000.795227
EM: Round [399] log likelihood: -2000.794699
EM: Round [400] log likelihood: -2000.794172
EM: Round [401] log likelihood: -2000.793646
EM: Round [402] log likelihood: -2000.793120
EM: Round [403] log likelihood: -2000.792595
EM: Round [404] log likelihood: -2000.792071
EM: Round [405] log likelihood: -2000.791548
EM: Round [406] log likelihood: -2000.791025
EM: Round [407] log likelihood: -2000.790503
EM: Round [408] log likelihood: -2000.789982
EM: Round [409] log likelihood: -2000.789462
EM: Round [410] log likelihood: -2000.788943
EM: Round [411] log likelihood: -2000.788424
EM: Round [412] log likelihood: -2000.787906
EM: Round [413] log likelihood: -2000.787389
EM: Round [414] log likelihood: -2000.786872
EM: Round [415] log likelihood: -2000.786357
EM: Round [416] log likelihood: -2000.785842
EM: Round [417] log likelihood: -2000.785328
EM: Round [418] log likelihood: -2000.784814
EM: Round [419] log likelihood: -2000.784302
EM: Round [420] log likelihood: -2000.783790
EM: Round [421] log likelihood: -2000.783279
EM: Round [422] log likelihood: -2000.782768
EM: Round [423] log likelihood: -2000.782259
EM: Round [424] log likelihood: -2000.781750
EM: Round [425] log likelihood: -2000.781242
EM: Round [426] log likelihood: -2000.780735
EM: Round [427] log likelihood: -2000.780228
EM: Round [428] log likelihood: -2000.779722
EM: Round [429] log likelihood: -2000.779217
EM: Round [430] log likelihood: -2000.778713
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EM: Round [917] log likelihood: -2000.602471
EM: Round [918] log likelihood: -2000.602220
EM: Round [919] log likelihood: -2000.601969
EM: Round [920] log likelihood: -2000.601719
EM: Round [921] log likelihood: -2000.601469
EM: Round [922] log likelihood: -2000.601219
EM: Round [923] log likelihood: -2000.600969
EM: Round [924] log likelihood: -2000.600720
EM: Round [925] log likelihood: -2000.600472
EM: Round [926] log likelihood: -2000.600223
EM: Round [927] log likelihood: -2000.599975
EM: Round [928] log likelihood: -2000.599728
EM: Round [929] log likelihood: -2000.599480
EM: Round [930] log likelihood: -2000.599233
EM: Round [931] log likelihood: -2000.598987
EM: Round [932] log likelihood: -2000.598740
EM: Round [933] log likelihood: -2000.598494
EM: Round [934] log likelihood: -2000.598249
EM: Round [935] log likelihood: -2000.598003
EM: Round [936] log likelihood: -2000.597758
EM: Round [937] log likelihood: -2000.597514
EM: Round [938] log likelihood: -2000.597270
EM: Round [939] log likelihood: -2000.597026
EM: Round [940] log likelihood: -2000.596782
EM: Round [941] log likelihood: -2000.596539
EM: Round [942] log likelihood: -2000.596296
EM: Round [943] log likelihood: -2000.596053
EM: Round [944] log likelihood: -2000.595811
EM: Round [945] log likelihood: -2000.595569
EM: Round [946] log likelihood: -2000.595328
EM: Round [947] log likelihood: -2000.595086
EM: Round [948] log likelihood: -2000.594845
EM: Round [949] log likelihood: -2000.594605
EM: Round [950] log likelihood: -2000.594365
EM: Round [951] log likelihood: -2000.594125
EM: Round [952] log likelihood: -2000.593885
EM: Round [953] log likelihood: -2000.593646
EM: Round [954] log likelihood: -2000.593407
EM: Round [955] log likelihood: -2000.593169
EM: Round [956] log likelihood: -2000.592930
EM: Round [957] log likelihood: -2000.592692
EM: Round [958] log likelihood: -2000.592455
EM: Round [959] log likelihood: -2000.592218
EM: Round [960] log likelihood: -2000.591981
EM: Round [961] log likelihood: -2000.591744
EM: Round [962] log likelihood: -2000.591508
EM: Round [963] log likelihood: -2000.591272
EM: Round [964] log likelihood: -2000.591036
EM: Round [965] log likelihood: -2000.590801
EM: Round [966] log likelihood: -2000.590566
EM: Round [967] log likelihood: -2000.590331
EM: Round [968] log likelihood: -2000.590097
EM: Round [969] log likelihood: -2000.589863
EM: Round [970] log likelihood: -2000.589630
EM: Round [971] log likelihood: -2000.589396
EM: Round [972] log likelihood: -2000.589163
EM: Round [973] log likelihood: -2000.588930
EM: Round [974] log likelihood: -2000.588698
EM: Round [975] log likelihood: -2000.588466
EM: Round [976] log likelihood: -2000.588234
EM: Round [977] log likelihood: -2000.588003
EM: Round [978] log likelihood: -2000.587772
EM: Round [979] log likelihood: -2000.587541
EM: Round [980] log likelihood: -2000.587311
EM: Round [981] log likelihood: -2000.587081
EM: Round [982] log likelihood: -2000.586851
EM: Round [983] log likelihood: -2000.586621
EM: Round [984] log likelihood: -2000.586392
EM: Round [985] log likelihood: -2000.586163
EM: Round [986] log likelihood: -2000.585935
EM: Round [987] log likelihood: -2000.585707
EM: Round [988] log likelihood: -2000.585479
EM: Round [989] log likelihood: -2000.585251
EM: Round [990] log likelihood: -2000.585024
EM: Round [991] log likelihood: -2000.584797
EM: Round [992] log likelihood: -2000.584570
EM: Round [993] log likelihood: -2000.584344
EM: Round [994] log likelihood: -2000.584118
EM: Round [995] log likelihood: -2000.583892
EM: Round [996] log likelihood: -2000.583667
EM: Round [997] log likelihood: -2000.583442
EM: Round [998] log likelihood: -2000.583217
EM: Round [999] log likelihood: -2000.582992
EM: Round [1000] log likelihood: -2000.582768
EM: Round [1001] log likelihood: -2000.582544
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/tih_rna_sample_00760_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa > /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1471.053203
EM: Round [1] log likelihood: -1471.040550
EM: Round [2] log likelihood: -1471.040412
EM: Round [3] log likelihood: -1471.040410
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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz: 239789527
Execution Time = 4.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa --gtf /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fa --gtf /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf > /tmp/nxf.bkEML7IVg5/fi_workdir/microH.dat
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.bkEML7IVg5/fi_workdir/microH.dat /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/microH.dat /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bkEML7IVg5 --json_outfile /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00760_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bkEML7IVg5 --json_outfile /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00760_B23MVV7LT4_1
Running: touch /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00760_B23MVV7LT4_1 --html_output /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00760_B23MVV7LT4_1 --html_output /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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 [ENSG00000280136.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bkEML7IVg5/ctat_genome_lib_build_dir > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.bkEML7IVg5/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory