Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/edff5862a5cfe39efcfa0f24b389e8/tih_rna_sample_00434_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/c2c00ac6047337ad4d6f2d2e44a0c8/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/c2c00ac6047337ad4d6f2d2e44a0c8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/1a11c12935f6aa87df5bfd575078cf/tih_rna_sample_00434_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/1a11c12935f6aa87df5bfd575078cf/tih_rna_sample_00434_B23WHTKLT4_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_00434_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00434_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/cytoBand.txt
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00434_B23WHTKLT4_1.star --out_dir /tmp/nxf.hsK8Wg1IOC/fi_workdir --reads "/tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:17:03 ..... started STAR run
Jun 08 10:17:03 ..... loading genome
Jun 08 10:18:46 ... generating Suffix Array index
Jun 08 10:22:37 ... completed Suffix Array index
Jun 08 10:22:37 ..... processing annotations GTF
Jun 08 10:22:38 ..... inserting junctions into the genome indices
Jun 08 10:23:38 ..... started mapping
Jun 08 11:28:11 ..... finished mapping
Jun 08 11:28:13 ..... started sorting BAM
Jun 08 11:28:14 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 71.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00434_B23WHTKLT4_1.star --out_dir /tmp/nxf.hsK8Wg1IOC/fi_workdir --reads "/tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:28:17 : INFO : Done.
Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[540000] -done parsing /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 2031,
'num genes matched < 2' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'seq-similar region overlap' => 30,
'exons hit < 2' => 1,
'excessive soft clipping' => 3626,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 22,
'small anchor length' => 36,
' ** passed ** ' => 14838,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 28
};
-writing fusion junction support info.
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[64000] -fusion SPANNING read extraction for scaff: AC092666.1--DPP6
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[84000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[36000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 2222,
'seq similar region alignment' => 37886
};
Execution Time = 0.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2036.217615
EM: Round [1] log likelihood: -2036.102224
EM: Round [2] log likelihood: -2036.064765
EM: Round [3] log likelihood: -2036.028771
EM: Round [4] log likelihood: -2035.994167
EM: Round [5] log likelihood: -2035.960887
EM: Round [6] log likelihood: -2035.928864
EM: Round [7] log likelihood: -2035.898039
EM: Round [8] log likelihood: -2035.868356
EM: Round [9] log likelihood: -2035.839761
EM: Round [10] log likelihood: -2035.812206
EM: Round [11] log likelihood: -2035.785642
EM: Round [12] log likelihood: -2035.760027
EM: Round [13] log likelihood: -2035.735318
EM: Round [14] log likelihood: -2035.711477
EM: Round [15] log likelihood: -2035.688467
EM: Round [16] log likelihood: -2035.666252
EM: Round [17] log likelihood: -2035.644800
EM: Round [18] log likelihood: -2035.624079
EM: Round [19] log likelihood: -2035.604059
EM: Round [20] log likelihood: -2035.584713
EM: Round [21] log likelihood: -2035.566014
EM: Round [22] log likelihood: -2035.547935
EM: Round [23] log likelihood: -2035.530454
EM: Round [24] log likelihood: -2035.513546
EM: Round [25] log likelihood: -2035.497191
EM: Round [26] log likelihood: -2035.481366
EM: Round [27] log likelihood: -2035.466053
EM: Round [28] log likelihood: -2035.451232
EM: Round [29] log likelihood: -2035.436885
EM: Round [30] log likelihood: -2035.422996
EM: Round [31] log likelihood: -2035.409546
EM: Round [32] log likelihood: -2035.396521
EM: Round [33] log likelihood: -2035.383904
EM: Round [34] log likelihood: -2035.371683
EM: Round [35] log likelihood: -2035.359843
EM: Round [36] log likelihood: -2035.348370
EM: Round [37] log likelihood: -2035.337252
EM: Round [38] log likelihood: -2035.326477
EM: Round [39] log likelihood: -2035.316032
EM: Round [40] log likelihood: -2035.305907
EM: Round [41] log likelihood: -2035.296091
EM: Round [42] log likelihood: -2035.286574
EM: Round [43] log likelihood: -2035.277345
EM: Round [44] log likelihood: -2035.268394
EM: Round [45] log likelihood: -2035.259714
EM: Round [46] log likelihood: -2035.251294
EM: Round [47] log likelihood: -2035.243126
EM: Round [48] log likelihood: -2035.235202
EM: Round [49] log likelihood: -2035.227515
EM: Round [50] log likelihood: -2035.220056
EM: Round [51] log likelihood: -2035.212818
EM: Round [52] log likelihood: -2035.205795
EM: Round [53] log likelihood: -2035.198978
EM: Round [54] log likelihood: -2035.192362
EM: Round [55] log likelihood: -2035.185941
EM: Round [56] log likelihood: -2035.179708
EM: Round [57] log likelihood: -2035.173658
EM: Round [58] log likelihood: -2035.167784
EM: Round [59] log likelihood: -2035.162081
EM: Round [60] log likelihood: -2035.156544
EM: Round [61] log likelihood: -2035.151168
EM: Round [62] log likelihood: -2035.145948
EM: Round [63] log likelihood: -2035.140879
EM: Round [64] log likelihood: -2035.135957
EM: Round [65] log likelihood: -2035.131176
EM: Round [66] log likelihood: -2035.126533
EM: Round [67] log likelihood: -2035.122024
EM: Round [68] log likelihood: -2035.117644
EM: Round [69] log likelihood: -2035.113389
EM: Round [70] log likelihood: -2035.109257
EM: Round [71] log likelihood: -2035.105242
EM: Round [72] log likelihood: -2035.101342
EM: Round [73] log likelihood: -2035.097554
EM: Round [74] log likelihood: -2035.093873
EM: Round [75] log likelihood: -2035.090297
EM: Round [76] log likelihood: -2035.086823
EM: Round [77] log likelihood: -2035.083447
EM: Round [78] log likelihood: -2035.080167
EM: Round [79] log likelihood: -2035.076980
EM: Round [80] log likelihood: -2035.073883
EM: Round [81] log likelihood: -2035.070874
EM: Round [82] log likelihood: -2035.067949
EM: Round [83] log likelihood: -2035.065107
EM: Round [84] log likelihood: -2035.062345
EM: Round [85] log likelihood: -2035.059661
EM: Round [86] log likelihood: -2035.057053
EM: Round [87] log likelihood: -2035.054517
EM: Round [88] log likelihood: -2035.052053
EM: Round [89] log likelihood: -2035.049658
EM: Round [90] log likelihood: -2035.047330
EM: Round [91] log likelihood: -2035.045068
EM: Round [92] log likelihood: -2035.042869
EM: Round [93] log likelihood: -2035.040731
EM: Round [94] log likelihood: -2035.038653
EM: Round [95] log likelihood: -2035.036633
EM: Round [96] log likelihood: -2035.034670
EM: Round [97] log likelihood: -2035.032761
EM: Round [98] log likelihood: -2035.030905
EM: Round [99] log likelihood: -2035.029101
EM: Round [100] log likelihood: -2035.027348
EM: Round [101] log likelihood: -2035.025643
EM: Round [102] log likelihood: -2035.023986
EM: Round [103] log likelihood: -2035.022375
EM: Round [104] log likelihood: -2035.020808
EM: Round [105] log likelihood: -2035.019285
EM: Round [106] log likelihood: -2035.017804
EM: Round [107] log likelihood: -2035.016365
EM: Round [108] log likelihood: -2035.014965
EM: Round [109] log likelihood: -2035.013604
EM: Round [110] log likelihood: -2035.012281
EM: Round [111] log likelihood: -2035.010994
EM: Round [112] log likelihood: -2035.009744
EM: Round [113] log likelihood: -2035.008527
EM: Round [114] log likelihood: -2035.007345
EM: Round [115] log likelihood: -2035.006195
EM: Round [116] log likelihood: -2035.005076
EM: Round [117] log likelihood: -2035.003989
EM: Round [118] log likelihood: -2035.002932
EM: Round [119] log likelihood: -2035.001904
EM: Round [120] log likelihood: -2035.000904
EM: Round [121] log likelihood: -2034.999932
EM: Round [122] log likelihood: -2034.998987
EM: Round [123] log likelihood: -2034.998068
EM: Round [124] log likelihood: -2034.997174
EM: Round [125] log likelihood: -2034.996304
EM: Round [126] log likelihood: -2034.995459
EM: Round [127] log likelihood: -2034.994637
EM: Round [128] log likelihood: -2034.993838
EM: Round [129] log likelihood: -2034.993060
EM: Round [130] log likelihood: -2034.992304
EM: Round [131] log likelihood: -2034.991569
EM: Round [132] log likelihood: -2034.990854
EM: Round [133] log likelihood: -2034.990159
EM: Round [134] log likelihood: -2034.989483
EM: Round [135] log likelihood: -2034.988825
EM: Round [136] log likelihood: -2034.988186
EM: Round [137] log likelihood: -2034.987564
EM: Round [138] log likelihood: -2034.986959
EM: Round [139] log likelihood: -2034.986371
EM: Round [140] log likelihood: -2034.985798
EM: Round [141] log likelihood: -2034.985242
EM: Round [142] log likelihood: -2034.984701
EM: Round [143] log likelihood: -2034.984175
EM: Round [144] log likelihood: -2034.983663
EM: Round [145] log likelihood: -2034.983165
EM: Round [146] log likelihood: -2034.982681
EM: Round [147] log likelihood: -2034.982210
EM: Round [148] log likelihood: -2034.981752
EM: Round [149] log likelihood: -2034.981307
EM: Round [150] log likelihood: -2034.980874
EM: Round [151] log likelihood: -2034.980452
EM: Round [152] log likelihood: -2034.980043
EM: Round [153] log likelihood: -2034.979644
EM: Round [154] log likelihood: -2034.979257
EM: Round [155] log likelihood: -2034.978880
EM: Round [156] log likelihood: -2034.978513
EM: Round [157] log likelihood: -2034.978156
EM: Round [158] log likelihood: -2034.977809
EM: Round [159] log likelihood: -2034.977472
EM: Round [160] log likelihood: -2034.977144
EM: Round [161] log likelihood: -2034.976825
EM: Round [162] log likelihood: -2034.976514
EM: Round [163] log likelihood: -2034.976213
EM: Round [164] log likelihood: -2034.975919
EM: Round [165] log likelihood: -2034.975633
EM: Round [166] log likelihood: -2034.975356
EM: Round [167] log likelihood: -2034.975085
EM: Round [168] log likelihood: -2034.974823
EM: Round [169] log likelihood: -2034.974567
EM: Round [170] log likelihood: -2034.974318
EM: Round [171] log likelihood: -2034.974077
EM: Round [172] log likelihood: -2034.973841
EM: Round [173] log likelihood: -2034.973613
EM: Round [174] log likelihood: -2034.973390
EM: Round [175] log likelihood: -2034.973174
EM: Round [176] log likelihood: -2034.972963
EM: Round [177] log likelihood: -2034.972758
EM: Round [178] log likelihood: -2034.972559
EM: Round [179] log likelihood: -2034.972366
EM: Round [180] log likelihood: -2034.972177
EM: Round [181] log likelihood: -2034.971994
EM: Round [182] log likelihood: -2034.971816
EM: Round [183] log likelihood: -2034.971642
EM: Round [184] log likelihood: -2034.971474
EM: Round [185] log likelihood: -2034.971310
EM: Round [186] log likelihood: -2034.971150
EM: Round [187] log likelihood: -2034.970995
EM: Round [188] log likelihood: -2034.970844
EM: Round [189] log likelihood: -2034.970697
EM: Round [190] log likelihood: -2034.970554
EM: Round [191] log likelihood: -2034.970415
EM: Round [192] log likelihood: -2034.970280
EM: Round [193] log likelihood: -2034.970149
EM: Round [194] log likelihood: -2034.970021
EM: Round [195] log likelihood: -2034.969897
EM: Round [196] log likelihood: -2034.969776
EM: Round [197] log likelihood: -2034.969658
EM: Round [198] log likelihood: -2034.969544
EM: Round [199] log likelihood: -2034.969432
EM: Round [200] log likelihood: -2034.969324
EM: Round [201] log likelihood: -2034.969219
EM: Round [202] log likelihood: -2034.969116
EM: Round [203] log likelihood: -2034.969017
EM: Stopping iterations at round 203 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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/tih_rna_sample_00434_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa > /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir
-done, see /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1498.743054
EM: Round [1] log likelihood: -1498.743054
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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz: 295645013
Execution Time = 5.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa --gtf /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fa --gtf /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf > /tmp/nxf.hsK8Wg1IOC/fi_workdir/microH.dat
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.hsK8Wg1IOC/fi_workdir/microH.dat /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.hsK8Wg1IOC/fi_workdir/microH.dat /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hsK8Wg1IOC --json_outfile /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00434_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.hsK8Wg1IOC --json_outfile /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00434_B23WHTKLT4_1
Running: touch /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00434_B23WHTKLT4_1 --html_output /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00434_B23WHTKLT4_1 --html_output /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.hsK8Wg1IOC/ctat_genome_lib_build_dir > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.hsK8Wg1IOC/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory