Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/68b7eef14742105927cf5be91e89b4/tih_rna_sample_00121_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/0b8eee8f9e7f900c5953d4571c6f85/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/0b8eee8f9e7f900c5953d4571c6f85/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/68b7eef14742105927cf5be91e89b4/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/5c524b3e858ab837f8a9e796a56c06/tih_rna_sample_00121_B23WHTKLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00121_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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_00121_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/cytoBand.txt
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00121_B23WHTKLT4_1.star --out_dir /tmp/nxf.us79jhaJOe/fi_workdir --reads "/tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.us79jhaJOe/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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:51:42 ..... started STAR run
Jun 08 09:51:42 ..... loading genome
Jun 08 09:53:23 ... generating Suffix Array index
Jun 08 09:57:07 ... completed Suffix Array index
Jun 08 09:57:07 ..... processing annotations GTF
Jun 08 09:57:07 ..... inserting junctions into the genome indices
Jun 08 09:58:08 ..... started mapping
Jun 08 10:58:16 ..... finished mapping
Jun 08 10:58:17 ..... started sorting BAM
Jun 08 10:58:17 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00121_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00121_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 66.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00121_B23WHTKLT4_1.star --out_dir /tmp/nxf.us79jhaJOe/fi_workdir --reads "/tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:58:23 : INFO : Done.
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[870000] -done parsing /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 137,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 42,
'small anchor length' => 56,
' ** passed ** ' => 2716,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 140,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'low complexity anchor region' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'excessive soft clipping' => 5927,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 30,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
'per_id < 96' => 3159,
'num genes matched < 2' => 2,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 32
};
-writing fusion junction support info.
Execution Time = 0.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[42000] -fusion SPANNING read extraction for scaff: INTS6--CDK8
[1000]
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[83000] -fusion SPANNING read extraction for scaff: LUC7L--PGAP6
[1000]
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[34000]
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[38000]
[39000] -fusion SPANNING read extraction for scaff: LUC7L--Z97634.1
[1000]
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[30000]
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[35000]
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[38000] -fusion SPANNING read extraction for scaff: N4BP2L2--WDR95P
[1000]
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[72000]
[73000]
[74000]
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[76000]
[77000]
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[79000]
[80000]
[81000] -fusion SPANNING read extraction for scaff: PCCA--DOCK9
[1000]
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[20000]
[21000]
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
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[4000]
[5000]
[6000]
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[8000]
[9000]
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[20000]
[21000]
[22000]
[23000]
[24000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
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[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
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[33000]
[34000]
[35000]
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[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000] -fusion SPANNING read extraction for scaff: RTN3--ATL3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
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[11000]
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[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
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[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000] -fusion SPANNING read extraction for scaff: TMBIM4--MSRB3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[13000]
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[16000]
[17000]
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[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000] -fusion SPANNING read extraction for scaff: UBR3--AC078883.1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 36963,
'seq similar region alignment' => 22663
};
Execution Time = 1.31 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3468.261377
EM: Round [1] log likelihood: -3467.182234
EM: Round [2] log likelihood: -3466.343222
EM: Round [3] log likelihood: -3465.637058
EM: Round [4] log likelihood: -3465.038980
EM: Round [5] log likelihood: -3464.529942
EM: Round [6] log likelihood: -3464.094920
EM: Round [7] log likelihood: -3463.721886
EM: Round [8] log likelihood: -3463.401093
EM: Round [9] log likelihood: -3463.124559
EM: Round [10] log likelihood: -3462.885689
EM: Round [11] log likelihood: -3462.678992
EM: Round [12] log likelihood: -3462.499869
EM: Round [13] log likelihood: -3462.344441
EM: Round [14] log likelihood: -3462.209426
EM: Round [15] log likelihood: -3462.092031
EM: Round [16] log likelihood: -3461.989872
EM: Round [17] log likelihood: -3461.900909
EM: Round [18] log likelihood: -3461.823390
EM: Round [19] log likelihood: -3461.755806
EM: Round [20] log likelihood: -3461.696858
EM: Round [21] log likelihood: -3461.645419
EM: Round [22] log likelihood: -3461.600519
EM: Round [23] log likelihood: -3461.561314
EM: Round [24] log likelihood: -3461.527073
EM: Round [25] log likelihood: -3461.497159
EM: Round [26] log likelihood: -3461.471022
EM: Round [27] log likelihood: -3461.448179
EM: Round [28] log likelihood: -3461.428214
EM: Round [29] log likelihood: -3461.410760
EM: Round [30] log likelihood: -3461.395501
EM: Round [31] log likelihood: -3461.382158
EM: Round [32] log likelihood: -3461.370491
EM: Round [33] log likelihood: -3461.360287
EM: Round [34] log likelihood: -3461.351364
EM: Round [35] log likelihood: -3461.343559
EM: Round [36] log likelihood: -3461.336732
EM: Round [37] log likelihood: -3461.330760
EM: Round [38] log likelihood: -3461.325537
EM: Round [39] log likelihood: -3461.320967
EM: Round [40] log likelihood: -3461.316970
EM: Round [41] log likelihood: -3461.313473
EM: Round [42] log likelihood: -3461.310413
EM: Round [43] log likelihood: -3461.307736
EM: Round [44] log likelihood: -3461.305394
EM: Round [45] log likelihood: -3461.303346
EM: Round [46] log likelihood: -3461.301553
EM: Round [47] log likelihood: -3461.299985
EM: Round [48] log likelihood: -3461.298612
EM: Round [49] log likelihood: -3461.297412
EM: Round [50] log likelihood: -3461.296361
EM: Round [51] log likelihood: -3461.295442
EM: Round [52] log likelihood: -3461.294638
EM: Round [53] log likelihood: -3461.293934
EM: Round [54] log likelihood: -3461.293319
EM: Round [55] log likelihood: -3461.292780
EM: Round [56] log likelihood: -3461.292309
EM: Round [57] log likelihood: -3461.291896
EM: Round [58] log likelihood: -3461.291535
EM: Round [59] log likelihood: -3461.291219
EM: Round [60] log likelihood: -3461.290943
EM: Round [61] log likelihood: -3461.290701
EM: Round [62] log likelihood: -3461.290490
EM: Round [63] log likelihood: -3461.290305
EM: Round [64] log likelihood: -3461.290143
EM: Round [65] log likelihood: -3461.290001
EM: Round [66] log likelihood: -3461.289877
EM: Round [67] log likelihood: -3461.289769
EM: Round [68] log likelihood: -3461.289674
EM: Stopping iterations at round 68 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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/tih_rna_sample_00121_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa > /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/tih_rna_sample_00121_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir
-done, see /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3381.944027
EM: Round [1] log likelihood: -3381.918992
EM: Round [2] log likelihood: -3381.918789
EM: Round [3] log likelihood: -3381.918787
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz: 295776955
Execution Time = 5.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa --gtf /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fa --gtf /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.gtf > /tmp/nxf.us79jhaJOe/fi_workdir/microH.dat
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.us79jhaJOe/fi_workdir/microH.dat /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/fi_workdir/microH.dat /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.us79jhaJOe --json_outfile /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00121_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.us79jhaJOe --json_outfile /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00121_B23WHTKLT4_1
Running: touch /tmp/nxf.us79jhaJOe/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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00121_B23WHTKLT4_1 --html_output /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_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.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00121_B23WHTKLT4_1 --html_output /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000251321.1]
WARNING, no entry stored in dbm for [ENSG00000251321.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000225205.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.us79jhaJOe/ctat_genome_lib_build_dir > /tmp/nxf.us79jhaJOe/tih_rna_sample_00121_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.us79jhaJOe/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory