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/d0/f3da565c0d3f8d2e5576b23f3c1874/tih_rna_sample_00116_23H5VFLT4_s36_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/fb5b1029ed8d8b10397bc926bb7639/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/fb5b1029ed8d8b10397bc926bb7639/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/431fe6c25ed042a5c6ee67825f3275/tih_rna_sample_00116_23H5VFLT4_s36.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/f3da565c0d3f8d2e5576b23f3c1874/tih_rna_sample_00116_23H5VFLT4_s36_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_00116_23H5VFLT4_s36.fusionreport.tsv --gtf /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00116_23H5VFLT4_s36.fusionreport.tsv --gtf /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/cytoBand.txt
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed
-parsing GTF file: /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.bed.sorted.bed.gz
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.bed.tabix.ok
Running: samtools faidx /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa --max_mate_dist 100000 -G /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --CPU 8 --out_prefix tih_rna_sample_00116_23H5VFLT4_s36.star --out_dir /tmp/nxf.R3SmTO1c36/fi_workdir --reads "/tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:42:51 ..... started STAR run
Jun 08 09:42:51 ..... loading genome
Jun 08 09:44:30 ... generating Suffix Array index
Jun 08 09:48:13 ... completed Suffix Array index
Jun 08 09:48:13 ..... processing annotations GTF
Jun 08 09:48:13 ..... inserting junctions into the genome indices
Jun 08 09:49:13 ..... started mapping
Jun 08 10:37:01 ..... finished mapping
Jun 08 10:37:03 ..... started sorting BAM
Jun 08 10:37:03 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam
Execution Time = 54.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fa --max_mate_dist 100000 -G /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --CPU 8 --out_prefix tih_rna_sample_00116_23H5VFLT4_s36.star --out_dir /tmp/nxf.R3SmTO1c36/fi_workdir --reads "/tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_2.fastp.fastq.gz"
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam -o /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --remove_dups
10:37:05 : INFO : Done.
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.sortedByCoord.out.bam -o /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf
-parsing /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam
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[270000] -done parsing /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 24,
'per_id < 96' => 1905,
'seq-similar region overlap' => 193,
' ** passed ** ' => 2310,
'num genes matched < 2' => 2,
'small anchor length' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 18,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 6,
'excessive soft clipping' => 3470
};
-writing fusion junction support info.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[37000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[98000] -fusion SPANNING read extraction for scaff: ZNF587--CLASRP
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 18934,
'lacks exon overlap' => 5272
};
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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -1656.805582
EM: Round [1] log likelihood: -1656.287130
EM: Round [2] log likelihood: -1655.821445
EM: Round [3] log likelihood: -1655.401864
EM: Round [4] log likelihood: -1655.022796
EM: Round [5] log likelihood: -1654.679514
EM: Round [6] log likelihood: -1654.367983
EM: Round [7] log likelihood: -1654.084735
EM: Round [8] log likelihood: -1653.826771
EM: Round [9] log likelihood: -1653.591481
EM: Round [10] log likelihood: -1653.376585
EM: Round [11] log likelihood: -1653.180076
EM: Round [12] log likelihood: -1653.000184
EM: Round [13] log likelihood: -1652.835342
EM: Round [14] log likelihood: -1652.684154
EM: Round [15] log likelihood: -1652.545377
EM: Round [16] log likelihood: -1652.417897
EM: Round [17] log likelihood: -1652.300716
EM: Round [18] log likelihood: -1652.192936
EM: Round [19] log likelihood: -1652.093746
EM: Round [20] log likelihood: -1652.002415
EM: Round [21] log likelihood: -1651.918280
EM: Round [22] log likelihood: -1651.840742
EM: Round [23] log likelihood: -1651.769255
EM: Round [24] log likelihood: -1651.703322
EM: Round [25] log likelihood: -1651.642492
EM: Round [26] log likelihood: -1651.586353
EM: Round [27] log likelihood: -1651.534528
EM: Round [28] log likelihood: -1651.486674
EM: Round [29] log likelihood: -1651.442475
EM: Round [30] log likelihood: -1651.401644
EM: Round [31] log likelihood: -1651.363917
EM: Round [32] log likelihood: -1651.329050
EM: Round [33] log likelihood: -1651.296822
EM: Round [34] log likelihood: -1651.267028
EM: Round [35] log likelihood: -1651.239480
EM: Round [36] log likelihood: -1651.214005
EM: Round [37] log likelihood: -1651.190445
EM: Round [38] log likelihood: -1651.168653
EM: Round [39] log likelihood: -1651.148494
EM: Round [40] log likelihood: -1651.129844
EM: Round [41] log likelihood: -1651.112589
EM: Round [42] log likelihood: -1651.096622
EM: Round [43] log likelihood: -1651.081847
EM: Round [44] log likelihood: -1651.068174
EM: Round [45] log likelihood: -1651.055519
EM: Round [46] log likelihood: -1651.043806
EM: Round [47] log likelihood: -1651.032965
EM: Round [48] log likelihood: -1651.022929
EM: Round [49] log likelihood: -1651.013639
EM: Round [50] log likelihood: -1651.005039
EM: Round [51] log likelihood: -1650.997077
EM: Round [52] log likelihood: -1650.989705
EM: Round [53] log likelihood: -1650.982880
EM: Round [54] log likelihood: -1650.976561
EM: Round [55] log likelihood: -1650.970710
EM: Round [56] log likelihood: -1650.965292
EM: Round [57] log likelihood: -1650.960276
EM: Round [58] log likelihood: -1650.955631
EM: Round [59] log likelihood: -1650.951329
EM: Round [60] log likelihood: -1650.947346
EM: Round [61] log likelihood: -1650.943657
EM: Round [62] log likelihood: -1650.940241
EM: Round [63] log likelihood: -1650.937078
EM: Round [64] log likelihood: -1650.934148
EM: Round [65] log likelihood: -1650.931435
EM: Round [66] log likelihood: -1650.928922
EM: Round [67] log likelihood: -1650.926595
EM: Round [68] log likelihood: -1650.924440
EM: Round [69] log likelihood: -1650.922444
EM: Round [70] log likelihood: -1650.920595
EM: Round [71] log likelihood: -1650.918883
EM: Round [72] log likelihood: -1650.917297
EM: Round [73] log likelihood: -1650.915828
EM: Round [74] log likelihood: -1650.914468
EM: Round [75] log likelihood: -1650.913208
EM: Round [76] log likelihood: -1650.912041
EM: Round [77] log likelihood: -1650.910960
EM: Round [78] log likelihood: -1650.909959
EM: Round [79] log likelihood: -1650.909032
EM: Round [80] log likelihood: -1650.908173
EM: Round [81] log likelihood: -1650.907378
EM: Round [82] log likelihood: -1650.906641
EM: Round [83] log likelihood: -1650.905959
EM: Round [84] log likelihood: -1650.905327
EM: Round [85] log likelihood: -1650.904742
EM: Round [86] log likelihood: -1650.904199
EM: Round [87] log likelihood: -1650.903697
EM: Round [88] log likelihood: -1650.903232
EM: Round [89] log likelihood: -1650.902801
EM: Round [90] log likelihood: -1650.902402
EM: Round [91] log likelihood: -1650.902032
EM: Round [92] log likelihood: -1650.901690
EM: Round [93] log likelihood: -1650.901373
EM: Round [94] log likelihood: -1650.901079
EM: Round [95] log likelihood: -1650.900807
EM: Round [96] log likelihood: -1650.900555
EM: Round [97] log likelihood: -1650.900322
EM: Round [98] log likelihood: -1650.900105
EM: Round [99] log likelihood: -1650.899905
EM: Round [100] log likelihood: -1650.899720
EM: Round [101] log likelihood: -1650.899548
EM: Round [102] log likelihood: -1650.899389
EM: Round [103] log likelihood: -1650.899241
EM: Round [104] log likelihood: -1650.899105
EM: Round [105] log likelihood: -1650.898978
EM: Round [106] log likelihood: -1650.898861
EM: Round [107] log likelihood: -1650.898752
EM: Round [108] log likelihood: -1650.898652
EM: Round [109] log likelihood: -1650.898559
EM: Stopping iterations at round 109 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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa - | samtools sort -@ 8 - -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa - | samtools sort -@ 8 - -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam"
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa - | samtools sort -@ 8 - -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa - | samtools sort -@ 8 - -o /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam || :
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/tih_rna_sample_00116_23H5VFLT4_s36.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.star.cSorted.dupsMarked.bam /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam into /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords
CMD: touch /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.frag_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.frag_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.consolidated.bam.frag_coords > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.FusionJuncSpan
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.Pfam.gff3
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.Pfam.gff3 > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.Pfam.gff3 > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.Pfam.bed
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.seqsimilar.gff3
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.seqsimilar.gff3 > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.seqsimilar.gff3 > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.igv.seqsimilar.bed
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa > /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36 --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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/tih_rna_sample_00116_23H5VFLT4_s36.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir
-done, see /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1577.000478
EM: Round [1] log likelihood: -1577.000478
EM: Stopping iterations at round 1 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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz: 296460757
Execution Time = 5.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36_1.fastp.fastq.gz /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa --gtf /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fa --gtf /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gtf > /tmp/nxf.R3SmTO1c36/fi_workdir/microH.dat
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.R3SmTO1c36/fi_workdir/microH.dat /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.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.R3SmTO1c36/fi_workdir/microH.dat /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.R3SmTO1c36 --json_outfile /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.json --file_prefix tih_rna_sample_00116_23H5VFLT4_s36
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.R3SmTO1c36 --json_outfile /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.json --file_prefix tih_rna_sample_00116_23H5VFLT4_s36
Running: touch /tmp/nxf.R3SmTO1c36/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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00116_23H5VFLT4_s36 --html_output /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 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.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00116_23H5VFLT4_s36 --html_output /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.fusion_inspector_web.html
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.R3SmTO1c36/ctat_genome_lib_build_dir > /tmp/nxf.R3SmTO1c36/tih_rna_sample_00116_23H5VFLT4_s36.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.R3SmTO1c36/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory