Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/379c278ff9118d0c3f0b0e2596daad/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/778ae520539280eb669aea218af052/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/778ae520539280eb669aea218af052/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/0f30e4eec4224a40a40eb46a017f47/tih_rna_sample_00624_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/379c278ff9118d0c3f0b0e2596daad/tih_rna_sample_00624_B23MVV7LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00624_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00624_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/cytoBand.txt
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00624_B23MVV7LT4_1.star --out_dir /tmp/nxf.YfmKDMcENe/fi_workdir --reads "/tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:43:00 ..... started STAR run
Jun 08 09:43:00 ..... loading genome
Jun 08 09:44:42 ... generating Suffix Array index
Jun 08 09:49:00 ... completed Suffix Array index
Jun 08 09:49:00 ..... processing annotations GTF
Jun 08 09:49:00 ..... inserting junctions into the genome indices
Jun 08 09:50:03 ..... started mapping
Jun 08 10:41:23 ..... finished mapping
Jun 08 10:41:25 ..... started sorting BAM
Jun 08 10:41:25 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 58.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00624_B23MVV7LT4_1.star --out_dir /tmp/nxf.YfmKDMcENe/fi_workdir --reads "/tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:41:33 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1290000] -done parsing /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 409,
'low complexity anchor region' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 103,
'small anchor length' => 57,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
' ** passed ** ' => 6476,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 177,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 198,
'excessive soft clipping' => 6689,
'exons hit < 2' => 3,
'per_id < 96' => 4052
};
-writing fusion junction support info.
Execution Time = 0.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[75000] -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1
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[8000] -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR
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[15000] -fusion SPANNING read extraction for scaff: LPGAT1--AC096645.1
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[91000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[75000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[94000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[84000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[68000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[88000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[165000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[44000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
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[10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[16000] -fusion SPANNING read extraction for scaff: UFL1--AL355143.1
[1000]
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[16000] -fusion SPANNING read extraction for scaff: UFL1--EEF1GP6
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 81467,
'lacks exon overlap' => 3141
};
Execution Time = 1.57 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3850.694002
EM: Round [1] log likelihood: -3848.044229
EM: Round [2] log likelihood: -3846.017350
EM: Round [3] log likelihood: -3844.305709
EM: Round [4] log likelihood: -3842.848975
EM: Round [5] log likelihood: -3841.602975
EM: Round [6] log likelihood: -3840.532780
EM: Round [7] log likelihood: -3839.610348
EM: Round [8] log likelihood: -3838.812897
EM: Round [9] log likelihood: -3838.121721
EM: Round [10] log likelihood: -3837.521334
EM: Round [11] log likelihood: -3836.998809
EM: Round [12] log likelihood: -3836.543291
EM: Round [13] log likelihood: -3836.145606
EM: Round [14] log likelihood: -3835.797964
EM: Round [15] log likelihood: -3835.493721
EM: Round [16] log likelihood: -3835.227187
EM: Round [17] log likelihood: -3834.993476
EM: Round [18] log likelihood: -3834.788373
EM: Round [19] log likelihood: -3834.608240
EM: Round [20] log likelihood: -3834.449925
EM: Round [21] log likelihood: -3834.310691
EM: Round [22] log likelihood: -3834.188162
EM: Round [23] log likelihood: -3834.080266
EM: Round [24] log likelihood: -3833.985199
EM: Round [25] log likelihood: -3833.901384
EM: Round [26] log likelihood: -3833.827444
EM: Round [27] log likelihood: -3833.762173
EM: Round [28] log likelihood: -3833.704519
EM: Round [29] log likelihood: -3833.653555
EM: Round [30] log likelihood: -3833.608473
EM: Round [31] log likelihood: -3833.568562
EM: Round [32] log likelihood: -3833.533197
EM: Round [33] log likelihood: -3833.501833
EM: Round [34] log likelihood: -3833.473987
EM: Round [35] log likelihood: -3833.449238
EM: Round [36] log likelihood: -3833.427214
EM: Round [37] log likelihood: -3833.407589
EM: Round [38] log likelihood: -3833.390076
EM: Round [39] log likelihood: -3833.374422
EM: Round [40] log likelihood: -3833.360406
EM: Round [41] log likelihood: -3833.347833
EM: Round [42] log likelihood: -3833.336530
EM: Round [43] log likelihood: -3833.326346
EM: Round [44] log likelihood: -3833.317149
EM: Round [45] log likelihood: -3833.308821
EM: Round [46] log likelihood: -3833.301259
EM: Round [47] log likelihood: -3833.294373
EM: Round [48] log likelihood: -3833.288083
EM: Round [49] log likelihood: -3833.282318
EM: Round [50] log likelihood: -3833.277017
EM: Round [51] log likelihood: -3833.272124
EM: Round [52] log likelihood: -3833.267593
EM: Round [53] log likelihood: -3833.263381
EM: Round [54] log likelihood: -3833.259451
EM: Round [55] log likelihood: -3833.255769
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EM: Round [969] log likelihood: -3832.713130
EM: Round [970] log likelihood: -3832.713009
EM: Round [971] log likelihood: -3832.712888
EM: Round [972] log likelihood: -3832.712768
EM: Round [973] log likelihood: -3832.712648
EM: Round [974] log likelihood: -3832.712528
EM: Round [975] log likelihood: -3832.712409
EM: Round [976] log likelihood: -3832.712290
EM: Round [977] log likelihood: -3832.712171
EM: Round [978] log likelihood: -3832.712052
EM: Round [979] log likelihood: -3832.711934
EM: Round [980] log likelihood: -3832.711816
EM: Round [981] log likelihood: -3832.711698
EM: Round [982] log likelihood: -3832.711581
EM: Round [983] log likelihood: -3832.711464
EM: Round [984] log likelihood: -3832.711347
EM: Round [985] log likelihood: -3832.711231
EM: Round [986] log likelihood: -3832.711115
EM: Round [987] log likelihood: -3832.710999
EM: Round [988] log likelihood: -3832.710883
EM: Round [989] log likelihood: -3832.710768
EM: Round [990] log likelihood: -3832.710653
EM: Round [991] log likelihood: -3832.710538
EM: Round [992] log likelihood: -3832.710424
EM: Round [993] log likelihood: -3832.710310
EM: Round [994] log likelihood: -3832.710196
EM: Round [995] log likelihood: -3832.710083
EM: Round [996] log likelihood: -3832.709969
EM: Round [997] log likelihood: -3832.709856
EM: Round [998] log likelihood: -3832.709744
EM: Round [999] log likelihood: -3832.709631
EM: Round [1000] log likelihood: -3832.709519
EM: Round [1001] log likelihood: -3832.709408
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/tih_rna_sample_00624_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa > /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir
-done, see /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1331.313153
EM: Round [1] log likelihood: -1331.270596
EM: Round [2] log likelihood: -1331.267795
EM: Round [3] log likelihood: -1331.265396
EM: Round [4] log likelihood: -1331.263012
EM: Round [5] log likelihood: -1331.260640
EM: Round [6] log likelihood: -1331.258280
EM: Round [7] log likelihood: -1331.255930
EM: Round [8] log likelihood: -1331.253592
EM: Round [9] log likelihood: -1331.251265
EM: Round [10] log likelihood: -1331.248949
EM: Round [11] log likelihood: -1331.246644
EM: Round [12] log likelihood: -1331.244350
EM: Round [13] log likelihood: -1331.242066
EM: Round [14] log likelihood: -1331.239794
EM: Round [15] log likelihood: -1331.237532
EM: Round [16] log likelihood: -1331.235280
EM: Round [17] log likelihood: -1331.233039
EM: Round [18] log likelihood: -1331.230809
EM: Round [19] log likelihood: -1331.228589
EM: Round [20] log likelihood: -1331.226379
EM: Round [21] log likelihood: -1331.224180
EM: Round [22] log likelihood: -1331.221990
EM: Round [23] log likelihood: -1331.219811
EM: Round [24] log likelihood: -1331.217642
EM: Round [25] log likelihood: -1331.215482
EM: Round [26] log likelihood: -1331.213333
EM: Round [27] log likelihood: -1331.211194
EM: Round [28] log likelihood: -1331.209064
EM: Round [29] log likelihood: -1331.206944
EM: Round [30] log likelihood: -1331.204833
EM: Round [31] log likelihood: -1331.202732
EM: Round [32] log likelihood: -1331.200641
EM: Round [33] log likelihood: -1331.198559
EM: Round [34] log likelihood: -1331.196486
EM: Round [35] log likelihood: -1331.194423
EM: Round [36] log likelihood: -1331.192369
EM: Round [37] log likelihood: -1331.190324
EM: Round [38] log likelihood: -1331.188288
EM: Round [39] log likelihood: -1331.186262
EM: Round [40] log likelihood: -1331.184244
EM: Round [41] log likelihood: -1331.182235
EM: Round [42] log likelihood: -1331.180235
EM: Round [43] log likelihood: -1331.178245
EM: Round [44] log likelihood: -1331.176262
EM: Round [45] log likelihood: -1331.174289
EM: Round [46] log likelihood: -1331.172324
EM: Round [47] log likelihood: -1331.170368
EM: Round [48] log likelihood: -1331.168420
EM: Round [49] log likelihood: -1331.166481
EM: Round [50] log likelihood: -1331.164551
EM: Round [51] log likelihood: -1331.162629
EM: Round [52] log likelihood: -1331.160715
EM: Round [53] log likelihood: -1331.158809
EM: Round [54] log likelihood: -1331.156912
EM: Round [55] log likelihood: -1331.155023
EM: Round [56] log likelihood: -1331.153142
EM: Round [57] log likelihood: -1331.151269
EM: Round [58] log likelihood: -1331.149404
EM: Round [59] log likelihood: -1331.147547
EM: Round [60] log likelihood: -1331.145699
EM: Round [61] log likelihood: -1331.143858
EM: Round [62] log likelihood: -1331.142024
EM: Round [63] log likelihood: -1331.140199
EM: Round [64] log likelihood: -1331.138382
EM: Round [65] log likelihood: -1331.136572
EM: Round [66] log likelihood: -1331.134770
EM: Round [67] log likelihood: -1331.132975
EM: Round [68] log likelihood: -1331.131188
EM: Round [69] log likelihood: -1331.129408
EM: Round [70] log likelihood: -1331.127636
EM: Round [71] log likelihood: -1331.125872
EM: Round [72] log likelihood: -1331.124115
EM: Round [73] log likelihood: -1331.122365
EM: Round [74] log likelihood: -1331.120622
EM: Round [75] log likelihood: -1331.118887
EM: Round [76] log likelihood: -1331.117159
EM: Round [77] log likelihood: -1331.115438
EM: Round [78] log likelihood: -1331.113724
EM: Round [79] log likelihood: -1331.112018
EM: Round [80] log likelihood: -1331.110318
EM: Round [81] log likelihood: -1331.108625
EM: Round [82] log likelihood: -1331.106940
EM: Round [83] log likelihood: -1331.105261
EM: Round [84] log likelihood: -1331.103589
EM: Round [85] log likelihood: -1331.101924
EM: Round [86] log likelihood: -1331.100266
EM: Round [87] log likelihood: -1331.098615
EM: Round [88] log likelihood: -1331.096970
EM: Round [89] log likelihood: -1331.095332
EM: Round [90] log likelihood: -1331.093701
EM: Round [91] log likelihood: -1331.092076
EM: Round [92] log likelihood: -1331.090458
EM: Round [93] log likelihood: -1331.088846
EM: Round [94] log likelihood: -1331.087241
EM: Round [95] log likelihood: -1331.085643
EM: Round [96] log likelihood: -1331.084051
EM: Round [97] log likelihood: -1331.082465
EM: Round [98] log likelihood: -1331.080885
EM: Round [99] log likelihood: -1331.079312
EM: Round [100] log likelihood: -1331.077745
EM: Round [101] log likelihood: -1331.076185
EM: Round [102] log likelihood: -1331.074631
EM: Round [103] log likelihood: -1331.073082
EM: Round [104] log likelihood: -1331.071540
EM: Round [105] log likelihood: -1331.070005
EM: Round [106] log likelihood: -1331.068475
EM: Round [107] log likelihood: -1331.066951
EM: Round [108] log likelihood: -1331.065433
EM: Round [109] log likelihood: -1331.063922
EM: Round [110] log likelihood: -1331.062416
EM: Round [111] log likelihood: -1331.060916
EM: Round [112] log likelihood: -1331.059422
EM: Round [113] log likelihood: -1331.057934
EM: Round [114] log likelihood: -1331.056451
EM: Round [115] log likelihood: -1331.054975
EM: Round [116] log likelihood: -1331.053504
EM: Round [117] log likelihood: -1331.052039
EM: Round [118] log likelihood: -1331.050580
EM: Round [119] log likelihood: -1331.049126
EM: Round [120] log likelihood: -1331.047678
EM: Round [121] log likelihood: -1331.046236
EM: Round [122] log likelihood: -1331.044799
EM: Round [123] log likelihood: -1331.043368
EM: Round [124] log likelihood: -1331.041942
EM: Round [125] log likelihood: -1331.040522
EM: Round [126] log likelihood: -1331.039107
EM: Round [127] log likelihood: -1331.037698
EM: Round [128] log likelihood: -1331.036294
EM: Round [129] log likelihood: -1331.034895
EM: Round [130] log likelihood: -1331.033502
EM: Round [131] log likelihood: -1331.032114
EM: Round [132] log likelihood: -1331.030731
EM: Round [133] log likelihood: -1331.029354
EM: Round [134] log likelihood: -1331.027982
EM: Round [135] log likelihood: -1331.026615
EM: Round [136] log likelihood: -1331.025253
EM: Round [137] log likelihood: -1331.023897
EM: Round [138] log likelihood: -1331.022545
EM: Round [139] log likelihood: -1331.021199
EM: Round [140] log likelihood: -1331.019858
EM: Round [141] log likelihood: -1331.018521
EM: Round [142] log likelihood: -1331.017190
EM: Round [143] log likelihood: -1331.015864
EM: Round [144] log likelihood: -1331.014543
EM: Round [145] log likelihood: -1331.013227
EM: Round [146] log likelihood: -1331.011915
EM: Round [147] log likelihood: -1331.010609
EM: Round [148] log likelihood: -1331.009307
EM: Round [149] log likelihood: -1331.008011
EM: Round [150] log likelihood: -1331.006719
EM: Round [151] log likelihood: -1331.005432
EM: Round [152] log likelihood: -1331.004150
EM: Round [153] log likelihood: -1331.002872
EM: Round [154] log likelihood: -1331.001599
EM: Round [155] log likelihood: -1331.000331
EM: Round [156] log likelihood: -1330.999068
EM: Round [157] log likelihood: -1330.997809
EM: Round [158] log likelihood: -1330.996555
EM: Round [159] log likelihood: -1330.995306
EM: Round [160] log likelihood: -1330.994061
EM: Round [161] log likelihood: -1330.992820
EM: Round [162] log likelihood: -1330.991585
EM: Round [163] log likelihood: -1330.990353
EM: Round [164] log likelihood: -1330.989127
EM: Round [165] log likelihood: -1330.987904
EM: Round [166] log likelihood: -1330.986687
EM: Round [167] log likelihood: -1330.985473
EM: Round [168] log likelihood: -1330.984264
EM: Round [169] log likelihood: -1330.983060
EM: Round [170] log likelihood: -1330.981860
EM: Round [171] log likelihood: -1330.980664
EM: Round [172] log likelihood: -1330.979473
EM: Round [173] log likelihood: -1330.978285
EM: Round [174] log likelihood: -1330.977103
EM: Round [175] log likelihood: -1330.975924
EM: Round [176] log likelihood: -1330.974750
EM: Round [177] log likelihood: -1330.973579
EM: Round [178] log likelihood: -1330.972414
EM: Round [179] log likelihood: -1330.971252
EM: Round [180] log likelihood: -1330.970094
EM: Round [181] log likelihood: -1330.968941
EM: Round [182] log likelihood: -1330.967792
EM: Round [183] log likelihood: -1330.966647
EM: Round [184] log likelihood: -1330.965505
EM: Round [185] log likelihood: -1330.964368
EM: Round [186] log likelihood: -1330.963236
EM: Round [187] log likelihood: -1330.962107
EM: Round [188] log likelihood: -1330.960982
EM: Round [189] log likelihood: -1330.959861
EM: Round [190] log likelihood: -1330.958744
EM: Round [191] log likelihood: -1330.957631
EM: Round [192] log likelihood: -1330.956522
EM: Round [193] log likelihood: -1330.955417
EM: Round [194] log likelihood: -1330.954316
EM: Round [195] log likelihood: -1330.953218
EM: Round [196] log likelihood: -1330.952125
EM: Round [197] log likelihood: -1330.951035
EM: Round [198] log likelihood: -1330.949950
EM: Round [199] log likelihood: -1330.948868
EM: Round [200] log likelihood: -1330.947790
EM: Round [201] log likelihood: -1330.946715
EM: Round [202] log likelihood: -1330.945645
EM: Round [203] log likelihood: -1330.944578
EM: Round [204] log likelihood: -1330.943515
EM: Round [205] log likelihood: -1330.942455
EM: Round [206] log likelihood: -1330.941400
EM: Round [207] log likelihood: -1330.940347
EM: Round [208] log likelihood: -1330.939299
EM: Round [209] log likelihood: -1330.938254
EM: Round [210] log likelihood: -1330.937213
EM: Round [211] log likelihood: -1330.936176
EM: Round [212] log likelihood: -1330.935142
EM: Round [213] log likelihood: -1330.934112
EM: Round [214] log likelihood: -1330.933085
EM: Round [215] log likelihood: -1330.932062
EM: Round [216] log likelihood: -1330.931042
EM: Round [217] log likelihood: -1330.930026
EM: Round [218] log likelihood: -1330.929013
EM: Round [219] log likelihood: -1330.928004
EM: Round [220] log likelihood: -1330.926998
EM: Round [221] log likelihood: -1330.925996
EM: Round [222] log likelihood: -1330.924997
EM: Round [223] log likelihood: -1330.924002
EM: Round [224] log likelihood: -1330.923010
EM: Round [225] log likelihood: -1330.922021
EM: Round [226] log likelihood: -1330.921036
EM: Round [227] log likelihood: -1330.920054
EM: Round [228] log likelihood: -1330.919076
EM: Round [229] log likelihood: -1330.918101
EM: Round [230] log likelihood: -1330.917129
EM: Round [231] log likelihood: -1330.916160
EM: Round [232] log likelihood: -1330.915195
EM: Round [233] log likelihood: -1330.914233
EM: Round [234] log likelihood: -1330.913274
EM: Round [235] log likelihood: -1330.912319
EM: Round [236] log likelihood: -1330.911367
EM: Round [237] log likelihood: -1330.910418
EM: Round [238] log likelihood: -1330.909472
EM: Round [239] log likelihood: -1330.908529
EM: Round [240] log likelihood: -1330.907590
EM: Round [241] log likelihood: -1330.906653
EM: Round [242] log likelihood: -1330.905720
EM: Round [243] log likelihood: -1330.904790
EM: Round [244] log likelihood: -1330.903864
EM: Round [245] log likelihood: -1330.902940
EM: Round [246] log likelihood: -1330.902019
EM: Round [247] log likelihood: -1330.901102
EM: Round [248] log likelihood: -1330.900187
EM: Round [249] log likelihood: -1330.899276
EM: Round [250] log likelihood: -1330.898367
EM: Round [251] log likelihood: -1330.897462
EM: Round [252] log likelihood: -1330.896559
EM: Round [253] log likelihood: -1330.895660
EM: Round [254] log likelihood: -1330.894764
EM: Round [255] log likelihood: -1330.893870
EM: Round [256] log likelihood: -1330.892980
EM: Round [257] log likelihood: -1330.892093
EM: Round [258] log likelihood: -1330.891208
EM: Round [259] log likelihood: -1330.890327
EM: Round [260] log likelihood: -1330.889448
EM: Round [261] log likelihood: -1330.888572
EM: Round [262] log likelihood: -1330.887699
EM: Round [263] log likelihood: -1330.886829
EM: Round [264] log likelihood: -1330.885962
EM: Round [265] log likelihood: -1330.885098
EM: Round [266] log likelihood: -1330.884237
EM: Round [267] log likelihood: -1330.883378
EM: Round [268] log likelihood: -1330.882522
EM: Round [269] log likelihood: -1330.881669
EM: Round [270] log likelihood: -1330.880819
EM: Round [271] log likelihood: -1330.879972
EM: Round [272] log likelihood: -1330.879127
EM: Round [273] log likelihood: -1330.878286
EM: Round [274] log likelihood: -1330.877447
EM: Round [275] log likelihood: -1330.876610
EM: Round [276] log likelihood: -1330.875777
EM: Round [277] log likelihood: -1330.874946
EM: Round [278] log likelihood: -1330.874118
EM: Round [279] log likelihood: -1330.873292
EM: Round [280] log likelihood: -1330.872470
EM: Round [281] log likelihood: -1330.871649
EM: Round [282] log likelihood: -1330.870832
EM: Round [283] log likelihood: -1330.870017
EM: Round [284] log likelihood: -1330.869205
EM: Round [285] log likelihood: -1330.868396
EM: Round [286] log likelihood: -1330.867589
EM: Round [287] log likelihood: -1330.866785
EM: Round [288] log likelihood: -1330.865983
EM: Round [289] log likelihood: -1330.865184
EM: Round [290] log likelihood: -1330.864387
EM: Round [291] log likelihood: -1330.863593
EM: Round [292] log likelihood: -1330.862802
EM: Round [293] log likelihood: -1330.862013
EM: Round [294] log likelihood: -1330.861227
EM: Round [295] log likelihood: -1330.860443
EM: Round [296] log likelihood: -1330.859662
EM: Round [297] log likelihood: -1330.858883
EM: Round [298] log likelihood: -1330.858107
EM: Round [299] log likelihood: -1330.857333
EM: Round [300] log likelihood: -1330.856562
EM: Round [301] log likelihood: -1330.855793
EM: Round [302] log likelihood: -1330.855027
EM: Round [303] log likelihood: -1330.854263
EM: Round [304] log likelihood: -1330.853502
EM: Round [305] log likelihood: -1330.852743
EM: Round [306] log likelihood: -1330.851986
EM: Round [307] log likelihood: -1330.851232
EM: Round [308] log likelihood: -1330.850480
EM: Round [309] log likelihood: -1330.849731
EM: Round [310] log likelihood: -1330.848984
EM: Round [311] log likelihood: -1330.848239
EM: Round [312] log likelihood: -1330.847497
EM: Round [313] log likelihood: -1330.846757
EM: Round [314] log likelihood: -1330.846020
EM: Round [315] log likelihood: -1330.845284
EM: Round [316] log likelihood: -1330.844552
EM: Round [317] log likelihood: -1330.843821
EM: Round [318] log likelihood: -1330.843093
EM: Round [319] log likelihood: -1330.842367
EM: Round [320] log likelihood: -1330.841643
EM: Round [321] log likelihood: -1330.840922
EM: Round [322] log likelihood: -1330.840203
EM: Round [323] log likelihood: -1330.839486
EM: Round [324] log likelihood: -1330.838771
EM: Round [325] log likelihood: -1330.838059
EM: Round [326] log likelihood: -1330.837349
EM: Round [327] log likelihood: -1330.836641
EM: Round [328] log likelihood: -1330.835935
EM: Round [329] log likelihood: -1330.835232
EM: Round [330] log likelihood: -1330.834530
EM: Round [331] log likelihood: -1330.833831
EM: Round [332] log likelihood: -1330.833135
EM: Round [333] log likelihood: -1330.832440
EM: Round [334] log likelihood: -1330.831747
EM: Round [335] log likelihood: -1330.831057
EM: Round [336] log likelihood: -1330.830369
EM: Round [337] log likelihood: -1330.829683
EM: Round [338] log likelihood: -1330.828999
EM: Round [339] log likelihood: -1330.828317
EM: Round [340] log likelihood: -1330.827637
EM: Round [341] log likelihood: -1330.826960
EM: Round [342] log likelihood: -1330.826284
EM: Round [343] log likelihood: -1330.825611
EM: Round [344] log likelihood: -1330.824940
EM: Round [345] log likelihood: -1330.824271
EM: Round [346] log likelihood: -1330.823604
EM: Round [347] log likelihood: -1330.822939
EM: Round [348] log likelihood: -1330.822276
EM: Round [349] log likelihood: -1330.821615
EM: Round [350] log likelihood: -1330.820956
EM: Round [351] log likelihood: -1330.820299
EM: Round [352] log likelihood: -1330.819644
EM: Round [353] log likelihood: -1330.818991
EM: Round [354] log likelihood: -1330.818341
EM: Round [355] log likelihood: -1330.817692
EM: Round [356] log likelihood: -1330.817045
EM: Round [357] log likelihood: -1330.816400
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EM: Round [816] log likelihood: -1330.652676
EM: Round [817] log likelihood: -1330.652497
EM: Round [818] log likelihood: -1330.652319
EM: Round [819] log likelihood: -1330.652142
EM: Round [820] log likelihood: -1330.651965
EM: Round [821] log likelihood: -1330.651788
EM: Round [822] log likelihood: -1330.651612
EM: Round [823] log likelihood: -1330.651436
EM: Round [824] log likelihood: -1330.651261
EM: Round [825] log likelihood: -1330.651087
EM: Round [826] log likelihood: -1330.650912
EM: Round [827] log likelihood: -1330.650738
EM: Round [828] log likelihood: -1330.650565
EM: Round [829] log likelihood: -1330.650392
EM: Round [830] log likelihood: -1330.650220
EM: Round [831] log likelihood: -1330.650048
EM: Round [832] log likelihood: -1330.649876
EM: Round [833] log likelihood: -1330.649705
EM: Round [834] log likelihood: -1330.649534
EM: Round [835] log likelihood: -1330.649364
EM: Round [836] log likelihood: -1330.649194
EM: Round [837] log likelihood: -1330.649025
EM: Round [838] log likelihood: -1330.648856
EM: Round [839] log likelihood: -1330.648687
EM: Round [840] log likelihood: -1330.648519
EM: Round [841] log likelihood: -1330.648352
EM: Round [842] log likelihood: -1330.648185
EM: Round [843] log likelihood: -1330.648018
EM: Round [844] log likelihood: -1330.647852
EM: Round [845] log likelihood: -1330.647686
EM: Round [846] log likelihood: -1330.647520
EM: Round [847] log likelihood: -1330.647355
EM: Round [848] log likelihood: -1330.647191
EM: Round [849] log likelihood: -1330.647027
EM: Round [850] log likelihood: -1330.646863
EM: Round [851] log likelihood: -1330.646700
EM: Round [852] log likelihood: -1330.646537
EM: Round [853] log likelihood: -1330.646374
EM: Round [854] log likelihood: -1330.646212
EM: Round [855] log likelihood: -1330.646051
EM: Round [856] log likelihood: -1330.645889
EM: Round [857] log likelihood: -1330.645729
EM: Round [858] log likelihood: -1330.645568
EM: Round [859] log likelihood: -1330.645408
EM: Round [860] log likelihood: -1330.645249
EM: Round [861] log likelihood: -1330.645090
EM: Round [862] log likelihood: -1330.644931
EM: Round [863] log likelihood: -1330.644773
EM: Round [864] log likelihood: -1330.644615
EM: Round [865] log likelihood: -1330.644457
EM: Round [866] log likelihood: -1330.644300
EM: Round [867] log likelihood: -1330.644144
EM: Round [868] log likelihood: -1330.643987
EM: Round [869] log likelihood: -1330.643832
EM: Round [870] log likelihood: -1330.643676
EM: Round [871] log likelihood: -1330.643521
EM: Round [872] log likelihood: -1330.643366
EM: Round [873] log likelihood: -1330.643212
EM: Round [874] log likelihood: -1330.643058
EM: Round [875] log likelihood: -1330.642905
EM: Round [876] log likelihood: -1330.642752
EM: Round [877] log likelihood: -1330.642599
EM: Round [878] log likelihood: -1330.642447
EM: Round [879] log likelihood: -1330.642295
EM: Round [880] log likelihood: -1330.642144
EM: Round [881] log likelihood: -1330.641993
EM: Round [882] log likelihood: -1330.641842
EM: Round [883] log likelihood: -1330.641692
EM: Round [884] log likelihood: -1330.641542
EM: Round [885] log likelihood: -1330.641392
EM: Round [886] log likelihood: -1330.641243
EM: Round [887] log likelihood: -1330.641094
EM: Round [888] log likelihood: -1330.640946
EM: Round [889] log likelihood: -1330.640798
EM: Round [890] log likelihood: -1330.640650
EM: Round [891] log likelihood: -1330.640503
EM: Round [892] log likelihood: -1330.640356
EM: Round [893] log likelihood: -1330.640210
EM: Round [894] log likelihood: -1330.640064
EM: Round [895] log likelihood: -1330.639918
EM: Round [896] log likelihood: -1330.639773
EM: Round [897] log likelihood: -1330.639628
EM: Round [898] log likelihood: -1330.639483
EM: Round [899] log likelihood: -1330.639339
EM: Round [900] log likelihood: -1330.639195
EM: Round [901] log likelihood: -1330.639052
EM: Round [902] log likelihood: -1330.638909
EM: Round [903] log likelihood: -1330.638766
EM: Round [904] log likelihood: -1330.638623
EM: Round [905] log likelihood: -1330.638481
EM: Round [906] log likelihood: -1330.638340
EM: Round [907] log likelihood: -1330.638199
EM: Round [908] log likelihood: -1330.638058
EM: Round [909] log likelihood: -1330.637917
EM: Round [910] log likelihood: -1330.637777
EM: Round [911] log likelihood: -1330.637637
EM: Round [912] log likelihood: -1330.637498
EM: Round [913] log likelihood: -1330.637359
EM: Round [914] log likelihood: -1330.637220
EM: Round [915] log likelihood: -1330.637081
EM: Round [916] log likelihood: -1330.636943
EM: Round [917] log likelihood: -1330.636806
EM: Round [918] log likelihood: -1330.636668
EM: Round [919] log likelihood: -1330.636531
EM: Round [920] log likelihood: -1330.636395
EM: Round [921] log likelihood: -1330.636259
EM: Round [922] log likelihood: -1330.636123
EM: Round [923] log likelihood: -1330.635987
EM: Round [924] log likelihood: -1330.635852
EM: Round [925] log likelihood: -1330.635717
EM: Round [926] log likelihood: -1330.635583
EM: Round [927] log likelihood: -1330.635448
EM: Round [928] log likelihood: -1330.635315
EM: Round [929] log likelihood: -1330.635181
EM: Round [930] log likelihood: -1330.635048
EM: Round [931] log likelihood: -1330.634915
EM: Round [932] log likelihood: -1330.634783
EM: Round [933] log likelihood: -1330.634650
EM: Round [934] log likelihood: -1330.634519
EM: Round [935] log likelihood: -1330.634387
EM: Round [936] log likelihood: -1330.634256
EM: Round [937] log likelihood: -1330.634125
EM: Round [938] log likelihood: -1330.633995
EM: Round [939] log likelihood: -1330.633865
EM: Round [940] log likelihood: -1330.633735
EM: Round [941] log likelihood: -1330.633606
EM: Round [942] log likelihood: -1330.633476
EM: Round [943] log likelihood: -1330.633348
EM: Round [944] log likelihood: -1330.633219
EM: Round [945] log likelihood: -1330.633091
EM: Round [946] log likelihood: -1330.632963
EM: Round [947] log likelihood: -1330.632836
EM: Round [948] log likelihood: -1330.632709
EM: Round [949] log likelihood: -1330.632582
EM: Round [950] log likelihood: -1330.632455
EM: Round [951] log likelihood: -1330.632329
EM: Round [952] log likelihood: -1330.632203
EM: Round [953] log likelihood: -1330.632078
EM: Round [954] log likelihood: -1330.631953
EM: Round [955] log likelihood: -1330.631828
EM: Round [956] log likelihood: -1330.631703
EM: Round [957] log likelihood: -1330.631579
EM: Round [958] log likelihood: -1330.631455
EM: Round [959] log likelihood: -1330.631332
EM: Round [960] log likelihood: -1330.631208
EM: Round [961] log likelihood: -1330.631085
EM: Round [962] log likelihood: -1330.630963
EM: Round [963] log likelihood: -1330.630840
EM: Round [964] log likelihood: -1330.630718
EM: Round [965] log likelihood: -1330.630597
EM: Round [966] log likelihood: -1330.630475
EM: Round [967] log likelihood: -1330.630354
EM: Round [968] log likelihood: -1330.630233
EM: Round [969] log likelihood: -1330.630113
EM: Round [970] log likelihood: -1330.629993
EM: Round [971] log likelihood: -1330.629873
EM: Round [972] log likelihood: -1330.629753
EM: Round [973] log likelihood: -1330.629634
EM: Round [974] log likelihood: -1330.629515
EM: Round [975] log likelihood: -1330.629396
EM: Round [976] log likelihood: -1330.629278
EM: Round [977] log likelihood: -1330.629160
EM: Round [978] log likelihood: -1330.629042
EM: Round [979] log likelihood: -1330.628925
EM: Round [980] log likelihood: -1330.628808
EM: Round [981] log likelihood: -1330.628691
EM: Round [982] log likelihood: -1330.628574
EM: Round [983] log likelihood: -1330.628458
EM: Round [984] log likelihood: -1330.628342
EM: Round [985] log likelihood: -1330.628226
EM: Round [986] log likelihood: -1330.628111
EM: Round [987] log likelihood: -1330.627996
EM: Round [988] log likelihood: -1330.627881
EM: Round [989] log likelihood: -1330.627767
EM: Round [990] log likelihood: -1330.627652
EM: Round [991] log likelihood: -1330.627539
EM: Round [992] log likelihood: -1330.627425
EM: Round [993] log likelihood: -1330.627312
EM: Round [994] log likelihood: -1330.627199
EM: Round [995] log likelihood: -1330.627086
EM: Round [996] log likelihood: -1330.626973
EM: Round [997] log likelihood: -1330.626861
EM: Round [998] log likelihood: -1330.626749
EM: Round [999] log likelihood: -1330.626638
EM: Round [1000] log likelihood: -1330.626526
EM: Round [1001] log likelihood: -1330.626415
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz: 222722746
Execution Time = 4.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa --gtf /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fa --gtf /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf > /tmp/nxf.YfmKDMcENe/fi_workdir/microH.dat
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.YfmKDMcENe/fi_workdir/microH.dat /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.YfmKDMcENe/fi_workdir/microH.dat /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.YfmKDMcENe --json_outfile /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00624_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.YfmKDMcENe --json_outfile /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00624_B23MVV7LT4_1
Running: touch /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00624_B23MVV7LT4_1 --html_output /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00624_B23MVV7LT4_1 --html_output /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.YfmKDMcENe/ctat_genome_lib_build_dir > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.YfmKDMcENe/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory