Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2d3468d81c579dfe34acb09d87a5b2/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/5034132953016fce324418fe21c9f6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/1d41559e2a4365b55d42a6eb472d99/tih_rna_sample_00569_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2d3468d81c579dfe34acb09d87a5b2/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/5034132953016fce324418fe21c9f6/.command.run
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00569_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00569_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/cytoBand.txt
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00569_B23MVV7LT4_1.star --out_dir /tmp/nxf.jfar3XoMy6/fi_workdir --reads "/tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:35:58 ..... started STAR run
Jun 08 10:35:58 ..... loading genome
Jun 08 10:37:40 ... generating Suffix Array index
Jun 08 10:41:22 ... completed Suffix Array index
Jun 08 10:41:22 ..... processing annotations GTF
Jun 08 10:41:23 ..... inserting junctions into the genome indices
Jun 08 10:42:24 ..... started mapping
Jun 08 11:39:17 ..... finished mapping
Jun 08 11:39:18 ..... started sorting BAM
Jun 08 11:39:20 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 63.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00569_B23MVV7LT4_1.star --out_dir /tmp/nxf.jfar3XoMy6/fi_workdir --reads "/tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:39:40 : INFO : Done.
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[3500000] -done parsing /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'exons hit < 2' => 11,
'small anchor length' => 23,
' ** passed ** ' => 7261,
'low complexity anchor region' => 1,
'num genes matched < 2' => 22,
'per_id < 96' => 10537,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 336,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 7,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 77,
'seq-similar region overlap' => 133,
'excessive soft clipping' => 16526
};
-writing fusion junction support info.
Execution Time = 1.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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-fusion SPANNING read extraction for scaff: AC023866.2--ALB
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[30000] -fusion SPANNING read extraction for scaff: ANXA8--VSTM4
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[74000] -fusion SPANNING read extraction for scaff: EXOC4--CHCHD3
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[38000] -fusion SPANNING read extraction for scaff: EXOC4--FP236383.3
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[7000] -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2
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[7000] -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2
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[21000] -fusion SPANNING read extraction for scaff: MED12L--PRKCA
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[12000] -fusion SPANNING read extraction for scaff: MRPL39--SLC4A4
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[10000] -fusion SPANNING read extraction for scaff: MTRF1LP2--GSDMC
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[446000] -fusion SPANNING read extraction for scaff: NOTCH2--SPAG17
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[16000] -fusion SPANNING read extraction for scaff: NXPE3--AC107297.1
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[16000] -fusion SPANNING read extraction for scaff: NXPE3--AC078828.1
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[71000] -fusion SPANNING read extraction for scaff: OR10Z1--CAPZB
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[36000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[39000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[38000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[15000] -fusion SPANNING read extraction for scaff: PCDHA9--PCDHAC2
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[18000] -fusion SPANNING read extraction for scaff: PCDHA9--PCDHAC1
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[17000] -fusion SPANNING read extraction for scaff: PCDHA9--PCDHA13
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[52000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[53000] -fusion SPANNING read extraction for scaff: PLXNA4--CNTNAP2
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[24000] -fusion SPANNING read extraction for scaff: ROR2--RABL3
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[24000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[1821000] -fusion SPANNING read extraction for scaff: WWTR1--KRT6A
[1000]
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[11000] -fusion SPANNING read extraction for scaff: ZNF488--VSTM4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 17868,
'seq similar region alignment' => 36861
};
Execution Time = 4.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -5697.128655
EM: Round [1] log likelihood: -5688.420879
EM: Round [2] log likelihood: -5685.020401
EM: Round [3] log likelihood: -5683.135521
EM: Round [4] log likelihood: -5681.877949
EM: Round [5] log likelihood: -5680.967729
EM: Round [6] log likelihood: -5680.278430
EM: Round [7] log likelihood: -5679.737227
EM: Round [8] log likelihood: -5679.297987
EM: Round [9] log likelihood: -5678.930391
EM: Round [10] log likelihood: -5678.614131
EM: Round [11] log likelihood: -5678.335420
EM: Round [12] log likelihood: -5678.084795
EM: Round [13] log likelihood: -5677.855694
EM: Round [14] log likelihood: -5677.643521
EM: Round [15] log likelihood: -5677.445023
EM: Round [16] log likelihood: -5677.257865
EM: Round [17] log likelihood: -5677.080351
EM: Round [18] log likelihood: -5676.911227
EM: Round [19] log likelihood: -5676.749550
EM: Round [20] log likelihood: -5676.594594
EM: Round [21] log likelihood: -5676.445787
EM: Round [22] log likelihood: -5676.302671
EM: Round [23] log likelihood: -5676.164866
EM: Round [24] log likelihood: -5676.032052
EM: Round [25] log likelihood: -5675.903954
EM: Round [26] log likelihood: -5675.780327
EM: Round [27] log likelihood: -5675.660957
EM: Round [28] log likelihood: -5675.545646
EM: Round [29] log likelihood: -5675.434214
EM: Round [30] log likelihood: -5675.326496
EM: Round [31] log likelihood: -5675.222337
EM: Round [32] log likelihood: -5675.121590
EM: Round [33] log likelihood: -5675.024120
EM: Round [34] log likelihood: -5674.929799
EM: Round [35] log likelihood: -5674.838503
EM: Round [36] log likelihood: -5674.750117
EM: Round [37] log likelihood: -5674.664531
EM: Round [38] log likelihood: -5674.581639
EM: Round [39] log likelihood: -5674.501343
EM: Round [40] log likelihood: -5674.423546
EM: Round [41] log likelihood: -5674.348157
EM: Round [42] log likelihood: -5674.275089
EM: Round [43] log likelihood: -5674.204259
EM: Round [44] log likelihood: -5674.135587
EM: Round [45] log likelihood: -5674.068996
EM: Round [46] log likelihood: -5674.004413
EM: Round [47] log likelihood: -5673.941768
EM: Round [48] log likelihood: -5673.880993
EM: Round [49] log likelihood: -5673.822024
EM: Round [50] log likelihood: -5673.764798
EM: Round [51] log likelihood: -5673.709257
EM: Round [52] log likelihood: -5673.655343
EM: Round [53] log likelihood: -5673.603001
EM: Round [54] log likelihood: -5673.552178
EM: Round [55] log likelihood: -5673.502823
EM: Round [56] log likelihood: -5673.454888
EM: Round [57] log likelihood: -5673.408325
EM: Round [58] log likelihood: -5673.363090
EM: Round [59] log likelihood: -5673.319139
EM: Round [60] log likelihood: -5673.276430
EM: Round [61] log likelihood: -5673.234923
EM: Round [62] log likelihood: -5673.194578
EM: Round [63] log likelihood: -5673.155359
EM: Round [64] log likelihood: -5673.117230
EM: Round [65] log likelihood: -5673.080155
EM: Round [66] log likelihood: -5673.044102
EM: Round [67] log likelihood: -5673.009037
EM: Round [68] log likelihood: -5672.974931
EM: Round [69] log likelihood: -5672.941752
EM: Round [70] log likelihood: -5672.909473
EM: Round [71] log likelihood: -5672.878064
EM: Round [72] log likelihood: -5672.847500
EM: Round [73] log likelihood: -5672.817754
EM: Round [74] log likelihood: -5672.788800
EM: Round [75] log likelihood: -5672.760615
EM: Round [76] log likelihood: -5672.733176
EM: Round [77] log likelihood: -5672.706459
EM: Round [78] log likelihood: -5672.680443
EM: Round [79] log likelihood: -5672.655107
EM: Round [80] log likelihood: -5672.630430
EM: Round [81] log likelihood: -5672.606393
EM: Round [82] log likelihood: -5672.582976
EM: Round [83] log likelihood: -5672.560161
EM: Round [84] log likelihood: -5672.537930
EM: Round [85] log likelihood: -5672.516267
EM: Round [86] log likelihood: -5672.495154
EM: Round [87] log likelihood: -5672.474575
EM: Round [88] log likelihood: -5672.454515
EM: Round [89] log likelihood: -5672.434959
EM: Round [90] log likelihood: -5672.415891
EM: Round [91] log likelihood: -5672.397299
EM: Round [92] log likelihood: -5672.379168
EM: Round [93] log likelihood: -5672.361484
EM: Round [94] log likelihood: -5672.344236
EM: Round [95] log likelihood: -5672.327411
EM: Round [96] log likelihood: -5672.310996
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Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir
-done, see /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4341.386119
EM: Round [1] log likelihood: -4338.384354
EM: Round [2] log likelihood: -4337.804658
EM: Round [3] log likelihood: -4337.710865
EM: Round [4] log likelihood: -4337.696333
EM: Round [5] log likelihood: -4337.692677
EM: Round [6] log likelihood: -4337.690395
EM: Round [7] log likelihood: -4337.688287
EM: Round [8] log likelihood: -4337.686209
EM: Round [9] log likelihood: -4337.684141
EM: Round [10] log likelihood: -4337.682082
EM: Round [11] log likelihood: -4337.680032
EM: Round [12] log likelihood: -4337.677990
EM: Round [13] log likelihood: -4337.675958
EM: Round [14] log likelihood: -4337.673933
EM: Round [15] log likelihood: -4337.671917
EM: Round [16] log likelihood: -4337.669909
EM: Round [17] log likelihood: -4337.667910
EM: Round [18] log likelihood: -4337.665919
EM: Round [19] log likelihood: -4337.663936
EM: Round [20] log likelihood: -4337.661961
EM: Round [21] log likelihood: -4337.659995
EM: Round [22] log likelihood: -4337.658037
EM: Round [23] log likelihood: -4337.656086
EM: Round [24] log likelihood: -4337.654144
EM: Round [25] log likelihood: -4337.652209
EM: Round [26] log likelihood: -4337.650282
EM: Round [27] log likelihood: -4337.648364
EM: Round [28] log likelihood: -4337.646453
EM: Round [29] log likelihood: -4337.644549
EM: Round [30] log likelihood: -4337.642654
EM: Round [31] log likelihood: -4337.640766
EM: Round [32] log likelihood: -4337.638886
EM: Round [33] log likelihood: -4337.637013
EM: Round [34] log likelihood: -4337.635148
EM: Round [35] log likelihood: -4337.633290
EM: Round [36] log likelihood: -4337.631440
EM: Round [37] log likelihood: -4337.629597
EM: Round [38] log likelihood: -4337.627761
EM: Round [39] log likelihood: -4337.625933
EM: Round [40] log likelihood: -4337.624112
EM: Round [41] log likelihood: -4337.622298
EM: Round [42] log likelihood: -4337.620491
EM: Round [43] log likelihood: -4337.618692
EM: Round [44] log likelihood: -4337.616899
EM: Round [45] log likelihood: -4337.615114
EM: Round [46] log likelihood: -4337.613335
EM: Round [47] log likelihood: -4337.611564
EM: Round [48] log likelihood: -4337.609800
EM: Round [49] log likelihood: -4337.608042
EM: Round [50] log likelihood: -4337.606291
EM: Round [51] log likelihood: -4337.604547
EM: Round [52] log likelihood: -4337.602810
EM: Round [53] log likelihood: -4337.601080
EM: Round [54] log likelihood: -4337.599356
EM: Round [55] log likelihood: -4337.597639
EM: Round [56] log likelihood: -4337.595929
EM: Round [57] log likelihood: -4337.594225
EM: Round [58] log likelihood: -4337.592528
EM: Round [59] log likelihood: -4337.590837
EM: Round [60] log likelihood: -4337.589153
EM: Round [61] log likelihood: -4337.587475
EM: Round [62] log likelihood: -4337.585804
EM: Round [63] log likelihood: -4337.584138
EM: Round [64] log likelihood: -4337.582480
EM: Round [65] log likelihood: -4337.580827
EM: Round [66] log likelihood: -4337.579181
EM: Round [67] log likelihood: -4337.577541
EM: Round [68] log likelihood: -4337.575908
EM: Round [69] log likelihood: -4337.574280
EM: Round [70] log likelihood: -4337.572659
EM: Round [71] log likelihood: -4337.571044
EM: Round [72] log likelihood: -4337.569434
EM: Round [73] log likelihood: -4337.567831
EM: Round [74] log likelihood: -4337.566234
EM: Round [75] log likelihood: -4337.564643
EM: Round [76] log likelihood: -4337.563058
EM: Round [77] log likelihood: -4337.561478
EM: Round [78] log likelihood: -4337.559905
EM: Round [79] log likelihood: -4337.558337
EM: Round [80] log likelihood: -4337.556775
EM: Round [81] log likelihood: -4337.555219
EM: Round [82] log likelihood: -4337.553669
EM: Round [83] log likelihood: -4337.552125
EM: Round [84] log likelihood: -4337.550586
EM: Round [85] log likelihood: -4337.549053
EM: Round [86] log likelihood: -4337.547525
EM: Round [87] log likelihood: -4337.546003
EM: Round [88] log likelihood: -4337.544487
EM: Round [89] log likelihood: -4337.542976
EM: Round [90] log likelihood: -4337.541471
EM: Round [91] log likelihood: -4337.539971
EM: Round [92] log likelihood: -4337.538477
EM: Round [93] log likelihood: -4337.536988
EM: Round [94] log likelihood: -4337.535505
EM: Round [95] log likelihood: -4337.534026
EM: Round [96] log likelihood: -4337.532554
EM: Round [97] log likelihood: -4337.531086
EM: Round [98] log likelihood: -4337.529624
EM: Round [99] log likelihood: -4337.528167
EM: Round [100] log likelihood: -4337.526716
EM: Round [101] log likelihood: -4337.525269
EM: Round [102] log likelihood: -4337.523828
EM: Round [103] log likelihood: -4337.522392
EM: Round [104] log likelihood: -4337.520961
EM: Round [105] log likelihood: -4337.519536
EM: Round [106] log likelihood: -4337.518115
EM: Round [107] log likelihood: -4337.516699
EM: Round [108] log likelihood: -4337.515289
EM: Round [109] log likelihood: -4337.513883
EM: Round [110] log likelihood: -4337.512483
EM: Round [111] log likelihood: -4337.511087
EM: Round [112] log likelihood: -4337.509696
EM: Round [113] log likelihood: -4337.508311
EM: Round [114] log likelihood: -4337.506930
EM: Round [115] log likelihood: -4337.505554
EM: Round [116] log likelihood: -4337.504183
EM: Round [117] log likelihood: -4337.502816
EM: Round [118] log likelihood: -4337.501455
EM: Round [119] log likelihood: -4337.500098
EM: Round [120] log likelihood: -4337.498746
EM: Round [121] log likelihood: -4337.497399
EM: Round [122] log likelihood: -4337.496056
EM: Round [123] log likelihood: -4337.494718
EM: Round [124] log likelihood: -4337.493385
EM: Round [125] log likelihood: -4337.492057
EM: Round [126] log likelihood: -4337.490733
EM: Round [127] log likelihood: -4337.489413
EM: Round [128] log likelihood: -4337.488098
EM: Round [129] log likelihood: -4337.486788
EM: Round [130] log likelihood: -4337.485482
EM: Round [131] log likelihood: -4337.484181
EM: Round [132] log likelihood: -4337.482884
EM: Round [133] log likelihood: -4337.481592
EM: Round [134] log likelihood: -4337.480304
EM: Round [135] log likelihood: -4337.479021
EM: Round [136] log likelihood: -4337.477742
EM: Round [137] log likelihood: -4337.476467
EM: Round [138] log likelihood: -4337.475197
EM: Round [139] log likelihood: -4337.473931
EM: Round [140] log likelihood: -4337.472669
EM: Round [141] log likelihood: -4337.471412
EM: Round [142] log likelihood: -4337.470159
EM: Round [143] log likelihood: -4337.468910
EM: Round [144] log likelihood: -4337.467666
EM: Round [145] log likelihood: -4337.466425
EM: Round [146] log likelihood: -4337.465189
EM: Round [147] log likelihood: -4337.463957
EM: Round [148] log likelihood: -4337.462729
EM: Round [149] log likelihood: -4337.461506
EM: Round [150] log likelihood: -4337.460286
EM: Round [151] log likelihood: -4337.459071
EM: Round [152] log likelihood: -4337.457859
EM: Round [153] log likelihood: -4337.456652
EM: Round [154] log likelihood: -4337.455449
EM: Round [155] log likelihood: -4337.454250
EM: Round [156] log likelihood: -4337.453055
EM: Round [157] log likelihood: -4337.451863
EM: Round [158] log likelihood: -4337.450676
EM: Round [159] log likelihood: -4337.449493
EM: Round [160] log likelihood: -4337.448313
EM: Round [161] log likelihood: -4337.447138
EM: Round [162] log likelihood: -4337.445967
EM: Round [163] log likelihood: -4337.444799
EM: Round [164] log likelihood: -4337.443635
EM: Round [165] log likelihood: -4337.442475
EM: Round [166] log likelihood: -4337.441319
EM: Round [167] log likelihood: -4337.440167
EM: Round [168] log likelihood: -4337.439019
EM: Round [169] log likelihood: -4337.437874
EM: Round [170] log likelihood: -4337.436733
EM: Round [171] log likelihood: -4337.435596
EM: Round [172] log likelihood: -4337.434462
EM: Round [173] log likelihood: -4337.433333
EM: Round [174] log likelihood: -4337.432207
EM: Round [175] log likelihood: -4337.431084
EM: Round [176] log likelihood: -4337.429966
EM: Round [177] log likelihood: -4337.428851
EM: Round [178] log likelihood: -4337.427739
EM: Round [179] log likelihood: -4337.426632
EM: Round [180] log likelihood: -4337.425527
EM: Round [181] log likelihood: -4337.424427
EM: Round [182] log likelihood: -4337.423330
EM: Round [183] log likelihood: -4337.422236
EM: Round [184] log likelihood: -4337.421147
EM: Round [185] log likelihood: -4337.420060
EM: Round [186] log likelihood: -4337.418977
EM: Round [187] log likelihood: -4337.417898
EM: Round [188] log likelihood: -4337.416822
EM: Round [189] log likelihood: -4337.415750
EM: Round [190] log likelihood: -4337.414681
EM: Round [191] log likelihood: -4337.413615
EM: Round [192] log likelihood: -4337.412553
EM: Round [193] log likelihood: -4337.411495
EM: Round [194] log likelihood: -4337.410439
EM: Round [195] log likelihood: -4337.409387
EM: Round [196] log likelihood: -4337.408339
EM: Round [197] log likelihood: -4337.407294
EM: Round [198] log likelihood: -4337.406252
EM: Round [199] log likelihood: -4337.405213
EM: Round [200] log likelihood: -4337.404178
EM: Round [201] log likelihood: -4337.403146
EM: Round [202] log likelihood: -4337.402117
EM: Round [203] log likelihood: -4337.401092
EM: Round [204] log likelihood: -4337.400070
EM: Round [205] log likelihood: -4337.399051
EM: Round [206] log likelihood: -4337.398035
EM: Round [207] log likelihood: -4337.397023
EM: Round [208] log likelihood: -4337.396013
EM: Round [209] log likelihood: -4337.395007
EM: Round [210] log likelihood: -4337.394004
EM: Round [211] log likelihood: -4337.393005
EM: Round [212] log likelihood: -4337.392008
EM: Round [213] log likelihood: -4337.391015
EM: Round [214] log likelihood: -4337.390024
EM: Round [215] log likelihood: -4337.389037
EM: Round [216] log likelihood: -4337.388053
EM: Round [217] log likelihood: -4337.387072
EM: Round [218] log likelihood: -4337.386094
EM: Round [219] log likelihood: -4337.385119
EM: Round [220] log likelihood: -4337.384147
EM: Round [221] log likelihood: -4337.383178
EM: Round [222] log likelihood: -4337.382212
EM: Round [223] log likelihood: -4337.381249
EM: Round [224] log likelihood: -4337.380289
EM: Round [225] log likelihood: -4337.379333
EM: Round [226] log likelihood: -4337.378379
EM: Round [227] log likelihood: -4337.377428
EM: Round [228] log likelihood: -4337.376480
EM: Round [229] log likelihood: -4337.375535
EM: Round [230] log likelihood: -4337.374593
EM: Round [231] log likelihood: -4337.373653
EM: Round [232] log likelihood: -4337.372717
EM: Round [233] log likelihood: -4337.371783
EM: Round [234] log likelihood: -4337.370853
EM: Round [235] log likelihood: -4337.369925
EM: Round [236] log likelihood: -4337.369000
EM: Round [237] log likelihood: -4337.368078
EM: Round [238] log likelihood: -4337.367159
EM: Round [239] log likelihood: -4337.366243
EM: Round [240] log likelihood: -4337.365329
EM: Round [241] log likelihood: -4337.364418
EM: Round [242] log likelihood: -4337.363510
EM: Round [243] log likelihood: -4337.362605
EM: Round [244] log likelihood: -4337.361703
EM: Round [245] log likelihood: -4337.360803
EM: Round [246] log likelihood: -4337.359906
EM: Round [247] log likelihood: -4337.359012
EM: Round [248] log likelihood: -4337.358120
EM: Round [249] log likelihood: -4337.357232
EM: Round [250] log likelihood: -4337.356345
EM: Round [251] log likelihood: -4337.355462
EM: Round [252] log likelihood: -4337.354581
EM: Round [253] log likelihood: -4337.353703
EM: Round [254] log likelihood: -4337.352828
EM: Round [255] log likelihood: -4337.351955
EM: Round [256] log likelihood: -4337.351085
EM: Round [257] log likelihood: -4337.350217
EM: Round [258] log likelihood: -4337.349352
EM: Round [259] log likelihood: -4337.348490
EM: Round [260] log likelihood: -4337.347631
EM: Round [261] log likelihood: -4337.346773
EM: Round [262] log likelihood: -4337.345919
EM: Round [263] log likelihood: -4337.345067
EM: Round [264] log likelihood: -4337.344217
EM: Round [265] log likelihood: -4337.343371
EM: Round [266] log likelihood: -4337.342526
EM: Round [267] log likelihood: -4337.341684
EM: Round [268] log likelihood: -4337.340845
EM: Round [269] log likelihood: -4337.340008
EM: Round [270] log likelihood: -4337.339174
EM: Round [271] log likelihood: -4337.338342
EM: Round [272] log likelihood: -4337.337513
EM: Round [273] log likelihood: -4337.336686
EM: Round [274] log likelihood: -4337.335862
EM: Round [275] log likelihood: -4337.335040
EM: Round [276] log likelihood: -4337.334220
EM: Round [277] log likelihood: -4337.333403
EM: Round [278] log likelihood: -4337.332589
EM: Round [279] log likelihood: -4337.331776
EM: Round [280] log likelihood: -4337.330966
EM: Round [281] log likelihood: -4337.330159
EM: Round [282] log likelihood: -4337.329354
EM: Round [283] log likelihood: -4337.328551
EM: Round [284] log likelihood: -4337.327751
EM: Round [285] log likelihood: -4337.326953
EM: Round [286] log likelihood: -4337.326157
EM: Round [287] log likelihood: -4337.325364
EM: Round [288] log likelihood: -4337.324573
EM: Round [289] log likelihood: -4337.323785
EM: Round [290] log likelihood: -4337.322998
EM: Round [291] log likelihood: -4337.322214
EM: Round [292] log likelihood: -4337.321433
EM: Round [293] log likelihood: -4337.320653
EM: Round [294] log likelihood: -4337.319876
EM: Round [295] log likelihood: -4337.319101
EM: Round [296] log likelihood: -4337.318329
EM: Round [297] log likelihood: -4337.317558
EM: Round [298] log likelihood: -4337.316790
EM: Round [299] log likelihood: -4337.316025
EM: Round [300] log likelihood: -4337.315261
EM: Round [301] log likelihood: -4337.314500
EM: Round [302] log likelihood: -4337.313740
EM: Round [303] log likelihood: -4337.312983
EM: Round [304] log likelihood: -4337.312229
EM: Round [305] log likelihood: -4337.311476
EM: Round [306] log likelihood: -4337.310726
EM: Round [307] log likelihood: -4337.309978
EM: Round [308] log likelihood: -4337.309232
EM: Round [309] log likelihood: -4337.308488
EM: Round [310] log likelihood: -4337.307746
EM: Round [311] log likelihood: -4337.307006
EM: Round [312] log likelihood: -4337.306269
EM: Round [313] log likelihood: -4337.305534
EM: Round [314] log likelihood: -4337.304800
EM: Round [315] log likelihood: -4337.304069
EM: Round [316] log likelihood: -4337.303340
EM: Round [317] log likelihood: -4337.302613
EM: Round [318] log likelihood: -4337.301889
EM: Round [319] log likelihood: -4337.301166
EM: Round [320] log likelihood: -4337.300445
EM: Round [321] log likelihood: -4337.299727
EM: Round [322] log likelihood: -4337.299010
EM: Round [323] log likelihood: -4337.298296
EM: Round [324] log likelihood: -4337.297583
EM: Round [325] log likelihood: -4337.296873
EM: Round [326] log likelihood: -4337.296164
EM: Round [327] log likelihood: -4337.295458
EM: Round [328] log likelihood: -4337.294754
EM: Round [329] log likelihood: -4337.294051
EM: Round [330] log likelihood: -4337.293351
EM: Round [331] log likelihood: -4337.292653
EM: Round [332] log likelihood: -4337.291957
EM: Round [333] log likelihood: -4337.291262
EM: Round [334] log likelihood: -4337.290570
EM: Round [335] log likelihood: -4337.289879
EM: Round [336] log likelihood: -4337.289191
EM: Round [337] log likelihood: -4337.288504
EM: Round [338] log likelihood: -4337.287820
EM: Round [339] log likelihood: -4337.287137
EM: Round [340] log likelihood: -4337.286457
EM: Round [341] log likelihood: -4337.285778
EM: Round [342] log likelihood: -4337.285101
EM: Round [343] log likelihood: -4337.284426
EM: Round [344] log likelihood: -4337.283753
EM: Round [345] log likelihood: -4337.283082
EM: Round [346] log likelihood: -4337.282413
EM: Round [347] log likelihood: -4337.281745
EM: Round [348] log likelihood: -4337.281080
EM: Round [349] log likelihood: -4337.280416
EM: Round [350] log likelihood: -4337.279755
EM: Round [351] log likelihood: -4337.279095
EM: Round [352] log likelihood: -4337.278437
EM: Round [353] log likelihood: -4337.277781
EM: Round [354] log likelihood: -4337.277126
EM: Round [355] log likelihood: -4337.276474
EM: Round [356] log likelihood: -4337.275823
EM: Round [357] log likelihood: -4337.275174
EM: Round [358] log likelihood: -4337.274527
EM: Round [359] log likelihood: -4337.273882
EM: Round [360] log likelihood: -4337.273239
EM: Round [361] log likelihood: -4337.272597
EM: Round [362] log likelihood: -4337.271957
EM: Round [363] log likelihood: -4337.271319
EM: Round [364] log likelihood: -4337.270683
EM: Round [365] log likelihood: -4337.270048
EM: Round [366] log likelihood: -4337.269416
EM: Round [367] log likelihood: -4337.268785
EM: Round [368] log likelihood: -4337.268156
EM: Round [369] log likelihood: -4337.267528
EM: Round [370] log likelihood: -4337.266902
EM: Round [371] log likelihood: -4337.266278
EM: Round [372] log likelihood: -4337.265656
EM: Round [373] log likelihood: -4337.265036
EM: Round [374] log likelihood: -4337.264417
EM: Round [375] log likelihood: -4337.263800
EM: Round [376] log likelihood: -4337.263184
EM: Round [377] log likelihood: -4337.262570
EM: Round [378] log likelihood: -4337.261958
EM: Round [379] log likelihood: -4337.261348
EM: Round [380] log likelihood: -4337.260740
EM: Round [381] log likelihood: -4337.260133
EM: Round [382] log likelihood: -4337.259527
EM: Round [383] log likelihood: -4337.258924
EM: Round [384] log likelihood: -4337.258322
EM: Round [385] log likelihood: -4337.257721
EM: Round [386] log likelihood: -4337.257123
EM: Round [387] log likelihood: -4337.256526
EM: Round [388] log likelihood: -4337.255930
EM: Round [389] log likelihood: -4337.255337
EM: Round [390] log likelihood: -4337.254745
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EM: Round [849] log likelihood: -4337.095681
EM: Round [850] log likelihood: -4337.095494
EM: Round [851] log likelihood: -4337.095307
EM: Round [852] log likelihood: -4337.095120
EM: Round [853] log likelihood: -4337.094934
EM: Round [854] log likelihood: -4337.094748
EM: Round [855] log likelihood: -4337.094563
EM: Round [856] log likelihood: -4337.094378
EM: Round [857] log likelihood: -4337.094193
EM: Round [858] log likelihood: -4337.094009
EM: Round [859] log likelihood: -4337.093826
EM: Round [860] log likelihood: -4337.093642
EM: Round [861] log likelihood: -4337.093460
EM: Round [862] log likelihood: -4337.093277
EM: Round [863] log likelihood: -4337.093095
EM: Round [864] log likelihood: -4337.092914
EM: Round [865] log likelihood: -4337.092733
EM: Round [866] log likelihood: -4337.092552
EM: Round [867] log likelihood: -4337.092372
EM: Round [868] log likelihood: -4337.092192
EM: Round [869] log likelihood: -4337.092013
EM: Round [870] log likelihood: -4337.091834
EM: Round [871] log likelihood: -4337.091655
EM: Round [872] log likelihood: -4337.091477
EM: Round [873] log likelihood: -4337.091299
EM: Round [874] log likelihood: -4337.091122
EM: Round [875] log likelihood: -4337.090945
EM: Round [876] log likelihood: -4337.090769
EM: Round [877] log likelihood: -4337.090593
EM: Round [878] log likelihood: -4337.090417
EM: Round [879] log likelihood: -4337.090242
EM: Round [880] log likelihood: -4337.090067
EM: Round [881] log likelihood: -4337.089892
EM: Round [882] log likelihood: -4337.089718
EM: Round [883] log likelihood: -4337.089545
EM: Round [884] log likelihood: -4337.089372
EM: Round [885] log likelihood: -4337.089199
EM: Round [886] log likelihood: -4337.089026
EM: Round [887] log likelihood: -4337.088854
EM: Round [888] log likelihood: -4337.088683
EM: Round [889] log likelihood: -4337.088511
EM: Round [890] log likelihood: -4337.088341
EM: Round [891] log likelihood: -4337.088170
EM: Round [892] log likelihood: -4337.088000
EM: Round [893] log likelihood: -4337.087831
EM: Round [894] log likelihood: -4337.087661
EM: Round [895] log likelihood: -4337.087492
EM: Round [896] log likelihood: -4337.087324
EM: Round [897] log likelihood: -4337.087156
EM: Round [898] log likelihood: -4337.086988
EM: Round [899] log likelihood: -4337.086821
EM: Round [900] log likelihood: -4337.086654
EM: Round [901] log likelihood: -4337.086488
EM: Round [902] log likelihood: -4337.086321
EM: Round [903] log likelihood: -4337.086156
EM: Round [904] log likelihood: -4337.085990
EM: Round [905] log likelihood: -4337.085825
EM: Round [906] log likelihood: -4337.085661
EM: Round [907] log likelihood: -4337.085496
EM: Round [908] log likelihood: -4337.085333
EM: Round [909] log likelihood: -4337.085169
EM: Round [910] log likelihood: -4337.085006
EM: Round [911] log likelihood: -4337.084843
EM: Round [912] log likelihood: -4337.084681
EM: Round [913] log likelihood: -4337.084519
EM: Round [914] log likelihood: -4337.084358
EM: Round [915] log likelihood: -4337.084196
EM: Round [916] log likelihood: -4337.084036
EM: Round [917] log likelihood: -4337.083875
EM: Round [918] log likelihood: -4337.083715
EM: Round [919] log likelihood: -4337.083555
EM: Round [920] log likelihood: -4337.083396
EM: Round [921] log likelihood: -4337.083237
EM: Round [922] log likelihood: -4337.083078
EM: Round [923] log likelihood: -4337.082920
EM: Round [924] log likelihood: -4337.082762
EM: Round [925] log likelihood: -4337.082605
EM: Round [926] log likelihood: -4337.082447
EM: Round [927] log likelihood: -4337.082291
EM: Round [928] log likelihood: -4337.082134
EM: Round [929] log likelihood: -4337.081978
EM: Round [930] log likelihood: -4337.081822
EM: Round [931] log likelihood: -4337.081667
EM: Round [932] log likelihood: -4337.081512
EM: Round [933] log likelihood: -4337.081357
EM: Round [934] log likelihood: -4337.081203
EM: Round [935] log likelihood: -4337.081049
EM: Round [936] log likelihood: -4337.080896
EM: Round [937] log likelihood: -4337.080742
EM: Round [938] log likelihood: -4337.080590
EM: Round [939] log likelihood: -4337.080437
EM: Round [940] log likelihood: -4337.080285
EM: Round [941] log likelihood: -4337.080133
EM: Round [942] log likelihood: -4337.079982
EM: Round [943] log likelihood: -4337.079831
EM: Round [944] log likelihood: -4337.079680
EM: Round [945] log likelihood: -4337.079529
EM: Round [946] log likelihood: -4337.079379
EM: Round [947] log likelihood: -4337.079230
EM: Round [948] log likelihood: -4337.079080
EM: Round [949] log likelihood: -4337.078931
EM: Round [950] log likelihood: -4337.078782
EM: Round [951] log likelihood: -4337.078634
EM: Round [952] log likelihood: -4337.078486
EM: Round [953] log likelihood: -4337.078338
EM: Round [954] log likelihood: -4337.078191
EM: Round [955] log likelihood: -4337.078044
EM: Round [956] log likelihood: -4337.077897
EM: Round [957] log likelihood: -4337.077751
EM: Round [958] log likelihood: -4337.077605
EM: Round [959] log likelihood: -4337.077460
EM: Round [960] log likelihood: -4337.077314
EM: Round [961] log likelihood: -4337.077169
EM: Round [962] log likelihood: -4337.077025
EM: Round [963] log likelihood: -4337.076880
EM: Round [964] log likelihood: -4337.076736
EM: Round [965] log likelihood: -4337.076593
EM: Round [966] log likelihood: -4337.076449
EM: Round [967] log likelihood: -4337.076306
EM: Round [968] log likelihood: -4337.076164
EM: Round [969] log likelihood: -4337.076021
EM: Round [970] log likelihood: -4337.075879
EM: Round [971] log likelihood: -4337.075738
EM: Round [972] log likelihood: -4337.075596
EM: Round [973] log likelihood: -4337.075455
EM: Round [974] log likelihood: -4337.075314
EM: Round [975] log likelihood: -4337.075174
EM: Round [976] log likelihood: -4337.075034
EM: Round [977] log likelihood: -4337.074894
EM: Round [978] log likelihood: -4337.074755
EM: Round [979] log likelihood: -4337.074616
EM: Round [980] log likelihood: -4337.074477
EM: Round [981] log likelihood: -4337.074338
EM: Round [982] log likelihood: -4337.074200
EM: Round [983] log likelihood: -4337.074062
EM: Round [984] log likelihood: -4337.073925
EM: Round [985] log likelihood: -4337.073788
EM: Round [986] log likelihood: -4337.073651
EM: Round [987] log likelihood: -4337.073514
EM: Round [988] log likelihood: -4337.073378
EM: Round [989] log likelihood: -4337.073242
EM: Round [990] log likelihood: -4337.073106
EM: Round [991] log likelihood: -4337.072971
EM: Round [992] log likelihood: -4337.072836
EM: Round [993] log likelihood: -4337.072701
EM: Round [994] log likelihood: -4337.072567
EM: Round [995] log likelihood: -4337.072433
EM: Round [996] log likelihood: -4337.072299
EM: Round [997] log likelihood: -4337.072165
EM: Round [998] log likelihood: -4337.072032
EM: Round [999] log likelihood: -4337.071899
EM: Round [1000] log likelihood: -4337.071767
EM: Round [1001] log likelihood: -4337.071634
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz: 296330273
Execution Time = 5.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa --gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa --gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/fi_workdir/microH.dat
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.jfar3XoMy6/fi_workdir/microH.dat /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/microH.dat /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.jfar3XoMy6 --json_outfile /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00569_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.jfar3XoMy6 --json_outfile /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00569_B23MVV7LT4_1
Running: touch /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00569_B23MVV7LT4_1 --html_output /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00569_B23MVV7LT4_1 --html_output /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
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 [ENSG00000123201.14]
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 [ENSG00000253784.1]
WARNING, no entry stored in dbm for [ENSG00000254222.1]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory