Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/d9a586dc4309ee0730bea86db4ebb0/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/41aae6e008b245dd54f7aeb878651e/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/53845c20b91947c2d2a6054de5b301/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/53845c20b91947c2d2a6054de5b301/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/d9a586dc4309ee0730bea86db4ebb0/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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 Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/cytoBand.txt
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed
-parsing GTF file: /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.e487RzRTjW/fi_workdir --reads "/tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.e487RzRTjW/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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:58:21 ..... started STAR run
Jun 08 09:58:21 ..... loading genome
Jun 08 10:00:08 ... generating Suffix Array index
Jun 08 10:04:00 ... completed Suffix Array index
Jun 08 10:04:01 ..... processing annotations GTF
Jun 08 10:04:01 ..... inserting junctions into the genome indices
Jun 08 10:05:02 ..... started mapping
Jun 08 11:09:03 ..... finished mapping
Jun 08 11:09:06 ..... started sorting BAM
Jun 08 11:09:09 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
Execution Time = 70.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.e487RzRTjW/fi_workdir --reads "/tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:09:46 : INFO : Done.
Execution Time = 0.51 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
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[5370000] -done parsing /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'excessive soft clipping' => 39245,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2,
'per_id < 96' => 31537,
'exons hit < 2' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
' ** passed ** ' => 46873,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 29,
'small anchor length' => 291,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 427,
'seq-similar region overlap' => 260,
'num genes matched < 2' => 53,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 60,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'low complexity anchor region' => 34,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
};
-writing fusion junction support info.
Execution Time = 3.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[46000] -fusion SPANNING read extraction for scaff: ERCC6L2--PPP1R9A-AS1
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[55000] -fusion SPANNING read extraction for scaff: FAF1--CDKN2C
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[38000] -fusion SPANNING read extraction for scaff: FAF1--MIR4421
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[184000] -fusion SPANNING read extraction for scaff: FOSL1--SLC30A8
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[47000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P4
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[52000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P6
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[125000] -fusion SPANNING read extraction for scaff: GTF2H2--FAM114A1
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[14000] -fusion SPANNING read extraction for scaff: LPAR1--SUSD1
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[133000] -fusion SPANNING read extraction for scaff: MMP24OS--PTPRT
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[67000] -fusion SPANNING read extraction for scaff: NEK10--CCBE1
-fusion SPANNING read extraction for scaff: NTM-AS1--OPCML
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[59000] -fusion SPANNING read extraction for scaff: PARD3--AL392046.1
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[4000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[83000] -fusion SPANNING read extraction for scaff: POLR2J3--KIF16B
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[33000] -fusion SPANNING read extraction for scaff: PSG9--CD177
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[54000] -fusion SPANNING read extraction for scaff: PSMB2--CELF4
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[179000] -fusion SPANNING read extraction for scaff: PXN--PLA2G1B
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[101000] -fusion SPANNING read extraction for scaff: RBBP4--FBXL2
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[13000] -fusion SPANNING read extraction for scaff: SDHAF3--AC025614.2
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[13000] -fusion SPANNING read extraction for scaff: SDHAF3--LINC01985
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[43000] -fusion SPANNING read extraction for scaff: SLC11A2--CASKP1
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[43000] -fusion SPANNING read extraction for scaff: SLC11A2--SFPQP1
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[14000] -fusion SPANNING read extraction for scaff: SLC30A7--UROC1
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[223000] -fusion SPANNING read extraction for scaff: SLC34A2--ROS1
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[71000] -fusion SPANNING read extraction for scaff: SMARCA2--TRIM72
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[53000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[132000] -fusion SPANNING read extraction for scaff: ST7--AC006001.3
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[54000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[29000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[1481000]
[1482000] -fusion SPANNING read extraction for scaff: TRIO--TMEM272
[1000]
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[67000]
[68000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[121000] -fusion SPANNING read extraction for scaff: UHRF2--SLC1A1
[1000]
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[10000] -fusion SPANNING read extraction for scaff: WWOX--AL591721.1
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[167000] -fusion SPANNING read extraction for scaff: XYLB--GOLGA4
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[89000] -fusion SPANNING read extraction for scaff: ZBTB40--ZMYM4
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[40000] -fusion SPANNING read extraction for scaff: ZFP62--SIMC1
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[16000] -fusion SPANNING read extraction for scaff: ZNF559--ZNF177
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 27008,
'lacks exon overlap' => 197274
};
Execution Time = 8.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -21931.055798
EM: Round [1] log likelihood: -21918.392121
EM: Round [2] log likelihood: -21915.830628
EM: Round [3] log likelihood: -21913.876513
EM: Round [4] log likelihood: -21912.331071
EM: Round [5] log likelihood: -21911.100037
EM: Round [6] log likelihood: -21910.113802
EM: Round [7] log likelihood: -21909.319452
EM: Round [8] log likelihood: -21908.676371
EM: Round [9] log likelihood: -21908.153142
EM: Round [10] log likelihood: -21907.725297
EM: Round [11] log likelihood: -21907.373677
EM: Round [12] log likelihood: -21907.083200
EM: Round [13] log likelihood: -21906.841944
EM: Round [14] log likelihood: -21906.640444
EM: Round [15] log likelihood: -21906.471159
EM: Round [16] log likelihood: -21906.328060
EM: Round [17] log likelihood: -21906.206311
EM: Round [18] log likelihood: -21906.102018
EM: Round [19] log likelihood: -21906.012042
EM: Round [20] log likelihood: -21905.933841
EM: Round [21] log likelihood: -21905.865350
EM: Round [22] log likelihood: -21905.804891
EM: Round [23] log likelihood: -21905.751093
EM: Round [24] log likelihood: -21905.702836
EM: Round [25] log likelihood: -21905.659200
EM: Round [26] log likelihood: -21905.619430
EM: Round [27] log likelihood: -21905.582903
EM: Round [28] log likelihood: -21905.549106
EM: Round [29] log likelihood: -21905.517611
EM: Round [30] log likelihood: -21905.488068
EM: Round [31] log likelihood: -21905.460182
EM: Round [32] log likelihood: -21905.433709
EM: Round [33] log likelihood: -21905.408446
EM: Round [34] log likelihood: -21905.384222
EM: Round [35] log likelihood: -21905.360895
EM: Round [36] log likelihood: -21905.338345
EM: Round [37] log likelihood: -21905.316472
EM: Round [38] log likelihood: -21905.295190
EM: Round [39] log likelihood: -21905.274429
EM: Round [40] log likelihood: -21905.254129
EM: Round [41] log likelihood: -21905.234238
EM: Round [42] log likelihood: -21905.214714
EM: Round [43] log likelihood: -21905.195519
EM: Round [44] log likelihood: -21905.176623
EM: Round [45] log likelihood: -21905.157998
EM: Round [46] log likelihood: -21905.139622
EM: Round [47] log likelihood: -21905.121476
EM: Round [48] log likelihood: -21905.103543
EM: Round [49] log likelihood: -21905.085809
EM: Round [50] log likelihood: -21905.068261
EM: Round [51] log likelihood: -21905.050888
EM: Round [52] log likelihood: -21905.033681
EM: Round [53] log likelihood: -21905.016633
EM: Round [54] log likelihood: -21904.999735
EM: Round [55] log likelihood: -21904.982982
EM: Round [56] log likelihood: -21904.966368
EM: Round [57] log likelihood: -21904.949889
EM: Round [58] log likelihood: -21904.933540
EM: Round [59] log likelihood: -21904.917317
EM: Round [60] log likelihood: -21904.901217
EM: Round [61] log likelihood: -21904.885236
EM: Round [62] log likelihood: -21904.869372
EM: Round [63] log likelihood: -21904.853622
EM: Round [64] log likelihood: -21904.837985
EM: Round [65] log likelihood: -21904.822456
EM: Round [66] log likelihood: -21904.807036
EM: Round [67] log likelihood: -21904.791721
EM: Round [68] log likelihood: -21904.776509
EM: Round [69] log likelihood: -21904.761400
EM: Round [70] log likelihood: -21904.746392
EM: Round [71] log likelihood: -21904.731483
EM: Round [72] log likelihood: -21904.716672
EM: Round [73] log likelihood: -21904.701957
EM: Round [74] log likelihood: -21904.687337
EM: Round [75] log likelihood: -21904.672810
EM: Round [76] log likelihood: -21904.658377
EM: Round [77] log likelihood: -21904.644034
EM: Round [78] log likelihood: -21904.629782
EM: Round [79] log likelihood: -21904.615620
EM: Round [80] log likelihood: -21904.601545
EM: Round [81] log likelihood: -21904.587557
EM: Round [82] log likelihood: -21904.573656
EM: Round [83] log likelihood: -21904.559839
EM: Round [84] log likelihood: -21904.546107
EM: Round [85] log likelihood: -21904.532458
EM: Round [86] log likelihood: -21904.518891
EM: Round [87] log likelihood: -21904.505406
EM: Round [88] log likelihood: -21904.492000
EM: Round [89] log likelihood: -21904.478675
EM: Round [90] log likelihood: -21904.465428
EM: Round [91] log likelihood: -21904.452259
EM: Round [92] log likelihood: -21904.439168
EM: Round [93] log likelihood: -21904.426152
EM: Round [94] log likelihood: -21904.413212
EM: Round [95] log likelihood: -21904.400347
EM: Round [96] log likelihood: -21904.387555
EM: Round [97] log likelihood: -21904.374837
EM: Round [98] log likelihood: -21904.362191
EM: Round [99] log likelihood: -21904.349617
EM: Round [100] log likelihood: -21904.337114
EM: Round [101] log likelihood: -21904.324681
EM: Round [102] log likelihood: -21904.312318
EM: Round [103] log likelihood: -21904.300024
EM: Round [104] log likelihood: -21904.287797
EM: Round [105] log likelihood: -21904.275639
EM: Round [106] log likelihood: -21904.263547
EM: Round [107] log likelihood: -21904.251522
EM: Round [108] log likelihood: -21904.239562
EM: Round [109] log likelihood: -21904.227667
EM: Round [110] log likelihood: -21904.215837
EM: Round [111] log likelihood: -21904.204070
EM: Round [112] log likelihood: -21904.192367
EM: Round [113] log likelihood: -21904.180726
EM: Round [114] log likelihood: -21904.169147
EM: Round [115] log likelihood: -21904.157630
EM: Round [116] log likelihood: -21904.146173
EM: Round [117] log likelihood: -21904.134777
EM: Round [118] log likelihood: -21904.123441
EM: Round [119] log likelihood: -21904.112164
EM: Round [120] log likelihood: -21904.100945
EM: Round [121] log likelihood: -21904.089785
EM: Round [122] log likelihood: -21904.078682
EM: Round [123] log likelihood: -21904.067636
EM: Round [124] log likelihood: -21904.056647
EM: Round [125] log likelihood: -21904.045714
EM: Round [126] log likelihood: -21904.034837
EM: Round [127] log likelihood: -21904.024015
EM: Round [128] log likelihood: -21904.013247
EM: Round [129] log likelihood: -21904.002534
EM: Round [130] log likelihood: -21903.991874
EM: Round [131] log likelihood: -21903.981268
EM: Round [132] log likelihood: -21903.970714
EM: Round [133] log likelihood: -21903.960213
EM: Round [134] log likelihood: -21903.949763
EM: Round [135] log likelihood: -21903.939365
EM: Round [136] log likelihood: -21903.929018
EM: Round [137] log likelihood: -21903.918722
EM: Round [138] log likelihood: -21903.908476
EM: Round [139] log likelihood: -21903.898280
EM: Round [140] log likelihood: -21903.888133
EM: Round [141] log likelihood: -21903.878034
EM: Round [142] log likelihood: -21903.867985
EM: Round [143] log likelihood: -21903.857984
EM: Round [144] log likelihood: -21903.848030
EM: Round [145] log likelihood: -21903.838124
EM: Round [146] log likelihood: -21903.828264
EM: Round [147] log likelihood: -21903.818452
EM: Round [148] log likelihood: -21903.808685
EM: Round [149] log likelihood: -21903.798965
EM: Round [150] log likelihood: -21903.789290
EM: Round [151] log likelihood: -21903.779660
EM: Round [152] log likelihood: -21903.770075
EM: Round [153] log likelihood: -21903.760534
EM: Round [154] log likelihood: -21903.751037
EM: Round [155] log likelihood: -21903.741584
EM: Round [156] log likelihood: -21903.732175
EM: Round [157] log likelihood: -21903.722809
EM: Round [158] log likelihood: -21903.713485
EM: Round [159] log likelihood: -21903.704204
EM: Round [160] log likelihood: -21903.694965
EM: Round [161] log likelihood: -21903.685767
EM: Round [162] log likelihood: -21903.676611
EM: Round [163] log likelihood: -21903.667497
EM: Round [164] log likelihood: -21903.658423
EM: Round [165] log likelihood: -21903.649389
EM: Round [166] log likelihood: -21903.640396
EM: Round [167] log likelihood: -21903.631443
EM: Round [168] log likelihood: -21903.622529
EM: Round [169] log likelihood: -21903.613655
EM: Round [170] log likelihood: -21903.604820
EM: Round [171] log likelihood: -21903.596023
EM: Round [172] log likelihood: -21903.587265
EM: Round [173] log likelihood: -21903.578546
EM: Round [174] log likelihood: -21903.569864
EM: Round [175] log likelihood: -21903.561220
EM: Round [176] log likelihood: -21903.552613
EM: Round [177] log likelihood: -21903.544043
EM: Round [178] log likelihood: -21903.535510
EM: Round [179] log likelihood: -21903.527014
EM: Round [180] log likelihood: -21903.518554
EM: Round [181] log likelihood: -21903.510130
EM: Round [182] log likelihood: -21903.501742
EM: Round [183] log likelihood: -21903.493390
EM: Round [184] log likelihood: -21903.485073
EM: Round [185] log likelihood: -21903.476791
EM: Round [186] log likelihood: -21903.468543
EM: Round [187] log likelihood: -21903.460331
EM: Round [188] log likelihood: -21903.452152
EM: Round [189] log likelihood: -21903.444008
EM: Round [190] log likelihood: -21903.435898
EM: Round [191] log likelihood: -21903.427821
EM: Round [192] log likelihood: -21903.419778
EM: Round [193] log likelihood: -21903.411768
EM: Round [194] log likelihood: -21903.403791
EM: Round [195] log likelihood: -21903.395847
EM: Round [196] log likelihood: -21903.387935
EM: Round [197] log likelihood: -21903.380056
EM: Round [198] log likelihood: -21903.372208
EM: Round [199] log likelihood: -21903.364393
EM: Round [200] log likelihood: -21903.356609
EM: Round [201] log likelihood: -21903.348857
EM: Round [202] log likelihood: -21903.341136
EM: Round [203] log likelihood: -21903.333445
EM: Round [204] log likelihood: -21903.325786
EM: Round [205] log likelihood: -21903.318158
EM: Round [206] log likelihood: -21903.310560
EM: Round [207] log likelihood: -21903.302992
EM: Round [208] log likelihood: -21903.295454
EM: Round [209] log likelihood: -21903.287946
EM: Round [210] log likelihood: -21903.280468
EM: Round [211] log likelihood: -21903.273019
EM: Round [212] log likelihood: -21903.265600
EM: Round [213] log likelihood: -21903.258209
EM: Round [214] log likelihood: -21903.250848
EM: Round [215] log likelihood: -21903.243515
EM: Round [216] log likelihood: -21903.236211
EM: Round [217] log likelihood: -21903.228935
EM: Round [218] log likelihood: -21903.221688
EM: Round [219] log likelihood: -21903.214468
EM: Round [220] log likelihood: -21903.207277
EM: Round [221] log likelihood: -21903.200113
EM: Round [222] log likelihood: -21903.192976
EM: Round [223] log likelihood: -21903.185867
EM: Round [224] log likelihood: -21903.178785
EM: Round [225] log likelihood: -21903.171730
EM: Round [226] log likelihood: -21903.164702
EM: Round [227] log likelihood: -21903.157701
EM: Round [228] log likelihood: -21903.150726
EM: Round [229] log likelihood: -21903.143777
EM: Round [230] log likelihood: -21903.136855
EM: Round [231] log likelihood: -21903.129959
EM: Round [232] log likelihood: -21903.123088
EM: Round [233] log likelihood: -21903.116244
EM: Round [234] log likelihood: -21903.109424
EM: Round [235] log likelihood: -21903.102631
EM: Round [236] log likelihood: -21903.095862
EM: Round [237] log likelihood: -21903.089119
EM: Round [238] log likelihood: -21903.082401
EM: Round [239] log likelihood: -21903.075707
EM: Round [240] log likelihood: -21903.069038
EM: Round [241] log likelihood: -21903.062394
EM: Round [242] log likelihood: -21903.055774
EM: Round [243] log likelihood: -21903.049178
EM: Round [244] log likelihood: -21903.042607
EM: Round [245] log likelihood: -21903.036059
EM: Round [246] log likelihood: -21903.029536
EM: Round [247] log likelihood: -21903.023036
EM: Round [248] log likelihood: -21903.016559
EM: Round [249] log likelihood: -21903.010106
EM: Round [250] log likelihood: -21903.003676
EM: Round [251] log likelihood: -21902.997270
EM: Round [252] log likelihood: -21902.990886
EM: Round [253] log likelihood: -21902.984525
EM: Round [254] log likelihood: -21902.978188
EM: Round [255] log likelihood: -21902.971872
EM: Round [256] log likelihood: -21902.965580
EM: Round [257] log likelihood: -21902.959309
EM: Round [258] log likelihood: -21902.953061
EM: Round [259] log likelihood: -21902.946835
EM: Round [260] log likelihood: -21902.940631
EM: Round [261] log likelihood: -21902.934449
EM: Round [262] log likelihood: -21902.928289
EM: Round [263] log likelihood: -21902.922150
EM: Round [264] log likelihood: -21902.916033
EM: Round [265] log likelihood: -21902.909938
EM: Round [266] log likelihood: -21902.903863
EM: Round [267] log likelihood: -21902.897810
EM: Round [268] log likelihood: -21902.891778
EM: Round [269] log likelihood: -21902.885767
EM: Round [270] log likelihood: -21902.879776
EM: Round [271] log likelihood: -21902.873807
EM: Round [272] log likelihood: -21902.867858
EM: Round [273] log likelihood: -21902.861929
EM: Round [274] log likelihood: -21902.856021
EM: Round [275] log likelihood: -21902.850133
EM: Round [276] log likelihood: -21902.844266
EM: Round [277] log likelihood: -21902.838418
EM: Round [278] log likelihood: -21902.832591
EM: Round [279] log likelihood: -21902.826783
EM: Round [280] log likelihood: -21902.820995
EM: Round [281] log likelihood: -21902.815227
EM: Round [282] log likelihood: -21902.809478
EM: Round [283] log likelihood: -21902.803748
EM: Round [284] log likelihood: -21902.798038
EM: Round [285] log likelihood: -21902.792348
EM: Round [286] log likelihood: -21902.786676
EM: Round [287] log likelihood: -21902.781023
EM: Round [288] log likelihood: -21902.775390
EM: Round [289] log likelihood: -21902.769775
EM: Round [290] log likelihood: -21902.764179
EM: Round [291] log likelihood: -21902.758602
EM: Round [292] log likelihood: -21902.753043
EM: Round [293] log likelihood: -21902.747502
EM: Round [294] log likelihood: -21902.741980
EM: Round [295] log likelihood: -21902.736477
EM: Round [296] log likelihood: -21902.730991
EM: Round [297] log likelihood: -21902.725524
EM: Round [298] log likelihood: -21902.720074
EM: Round [299] log likelihood: -21902.714643
EM: Round [300] log likelihood: -21902.709229
EM: Round [301] log likelihood: -21902.703833
EM: Round [302] log likelihood: -21902.698455
EM: Round [303] log likelihood: -21902.693094
EM: Round [304] log likelihood: -21902.687750
EM: Round [305] log likelihood: -21902.682424
EM: Round [306] log likelihood: -21902.677116
EM: Round [307] log likelihood: -21902.671824
EM: Round [308] log likelihood: -21902.666550
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EM: Round [767] log likelihood: -21901.289581
EM: Round [768] log likelihood: -21901.287917
EM: Round [769] log likelihood: -21901.286256
EM: Round [770] log likelihood: -21901.284598
EM: Round [771] log likelihood: -21901.282944
EM: Round [772] log likelihood: -21901.281293
EM: Round [773] log likelihood: -21901.279646
EM: Round [774] log likelihood: -21901.278002
EM: Round [775] log likelihood: -21901.276361
EM: Round [776] log likelihood: -21901.274724
EM: Round [777] log likelihood: -21901.273090
EM: Round [778] log likelihood: -21901.271460
EM: Round [779] log likelihood: -21901.269833
EM: Round [780] log likelihood: -21901.268209
EM: Round [781] log likelihood: -21901.266589
EM: Round [782] log likelihood: -21901.264972
EM: Round [783] log likelihood: -21901.263358
EM: Round [784] log likelihood: -21901.261748
EM: Round [785] log likelihood: -21901.260141
EM: Round [786] log likelihood: -21901.258537
EM: Round [787] log likelihood: -21901.256937
EM: Round [788] log likelihood: -21901.255340
EM: Round [789] log likelihood: -21901.253746
EM: Round [790] log likelihood: -21901.252155
EM: Round [791] log likelihood: -21901.250568
EM: Round [792] log likelihood: -21901.248984
EM: Round [793] log likelihood: -21901.247403
EM: Round [794] log likelihood: -21901.245825
EM: Round [795] log likelihood: -21901.244251
EM: Round [796] log likelihood: -21901.242680
EM: Round [797] log likelihood: -21901.241112
EM: Round [798] log likelihood: -21901.239547
EM: Round [799] log likelihood: -21901.237986
EM: Round [800] log likelihood: -21901.236427
EM: Round [801] log likelihood: -21901.234872
EM: Round [802] log likelihood: -21901.233320
EM: Round [803] log likelihood: -21901.231771
EM: Round [804] log likelihood: -21901.230225
EM: Round [805] log likelihood: -21901.228683
EM: Round [806] log likelihood: -21901.227143
EM: Round [807] log likelihood: -21901.225607
EM: Round [808] log likelihood: -21901.224074
EM: Round [809] log likelihood: -21901.222544
EM: Round [810] log likelihood: -21901.221017
EM: Round [811] log likelihood: -21901.219493
EM: Round [812] log likelihood: -21901.217972
EM: Round [813] log likelihood: -21901.216455
EM: Round [814] log likelihood: -21901.214940
EM: Round [815] log likelihood: -21901.213429
EM: Round [816] log likelihood: -21901.211920
EM: Round [817] log likelihood: -21901.210415
EM: Round [818] log likelihood: -21901.208912
EM: Round [819] log likelihood: -21901.207413
EM: Round [820] log likelihood: -21901.205917
EM: Round [821] log likelihood: -21901.204424
EM: Round [822] log likelihood: -21901.202933
EM: Round [823] log likelihood: -21901.201446
EM: Round [824] log likelihood: -21901.199962
EM: Round [825] log likelihood: -21901.198480
EM: Round [826] log likelihood: -21901.197002
EM: Round [827] log likelihood: -21901.195527
EM: Round [828] log likelihood: -21901.194055
EM: Round [829] log likelihood: -21901.192585
EM: Round [830] log likelihood: -21901.191119
EM: Round [831] log likelihood: -21901.189655
EM: Round [832] log likelihood: -21901.188195
EM: Round [833] log likelihood: -21901.186737
EM: Round [834] log likelihood: -21901.185282
EM: Round [835] log likelihood: -21901.183831
EM: Round [836] log likelihood: -21901.182382
EM: Round [837] log likelihood: -21901.180936
EM: Round [838] log likelihood: -21901.179493
EM: Round [839] log likelihood: -21901.178053
EM: Round [840] log likelihood: -21901.176615
EM: Round [841] log likelihood: -21901.175181
EM: Round [842] log likelihood: -21901.173749
EM: Round [843] log likelihood: -21901.172321
EM: Round [844] log likelihood: -21901.170895
EM: Round [845] log likelihood: -21901.169472
EM: Round [846] log likelihood: -21901.168052
EM: Round [847] log likelihood: -21901.166634
EM: Round [848] log likelihood: -21901.165220
EM: Round [849] log likelihood: -21901.163808
EM: Round [850] log likelihood: -21901.162399
EM: Round [851] log likelihood: -21901.160993
EM: Round [852] log likelihood: -21901.159590
EM: Round [853] log likelihood: -21901.158190
EM: Round [854] log likelihood: -21901.156792
EM: Round [855] log likelihood: -21901.155397
EM: Round [856] log likelihood: -21901.154005
EM: Round [857] log likelihood: -21901.152616
EM: Round [858] log likelihood: -21901.151229
EM: Round [859] log likelihood: -21901.149845
EM: Round [860] log likelihood: -21901.148464
EM: Round [861] log likelihood: -21901.147086
EM: Round [862] log likelihood: -21901.145710
EM: Round [863] log likelihood: -21901.144337
EM: Round [864] log likelihood: -21901.142967
EM: Round [865] log likelihood: -21901.141599
EM: Round [866] log likelihood: -21901.140234
EM: Round [867] log likelihood: -21901.138872
EM: Round [868] log likelihood: -21901.137513
EM: Round [869] log likelihood: -21901.136156
EM: Round [870] log likelihood: -21901.134802
EM: Round [871] log likelihood: -21901.133451
EM: Round [872] log likelihood: -21901.132102
EM: Round [873] log likelihood: -21901.130756
EM: Round [874] log likelihood: -21901.129413
EM: Round [875] log likelihood: -21901.128072
EM: Round [876] log likelihood: -21901.126734
EM: Round [877] log likelihood: -21901.125398
EM: Round [878] log likelihood: -21901.124065
EM: Round [879] log likelihood: -21901.122735
EM: Round [880] log likelihood: -21901.121407
EM: Round [881] log likelihood: -21901.120082
EM: Round [882] log likelihood: -21901.118760
EM: Round [883] log likelihood: -21901.117440
EM: Round [884] log likelihood: -21901.116123
EM: Round [885] log likelihood: -21901.114808
EM: Round [886] log likelihood: -21901.113496
EM: Round [887] log likelihood: -21901.112187
EM: Round [888] log likelihood: -21901.110880
EM: Round [889] log likelihood: -21901.109575
EM: Round [890] log likelihood: -21901.108274
EM: Round [891] log likelihood: -21901.106974
EM: Round [892] log likelihood: -21901.105678
EM: Round [893] log likelihood: -21901.104383
EM: Round [894] log likelihood: -21901.103092
EM: Round [895] log likelihood: -21901.101802
EM: Round [896] log likelihood: -21901.100516
EM: Round [897] log likelihood: -21901.099232
EM: Round [898] log likelihood: -21901.097950
EM: Round [899] log likelihood: -21901.096671
EM: Round [900] log likelihood: -21901.095394
EM: Round [901] log likelihood: -21901.094120
EM: Round [902] log likelihood: -21901.092848
EM: Round [903] log likelihood: -21901.091579
EM: Round [904] log likelihood: -21901.090312
EM: Round [905] log likelihood: -21901.089048
EM: Round [906] log likelihood: -21901.087786
EM: Round [907] log likelihood: -21901.086527
EM: Round [908] log likelihood: -21901.085270
EM: Round [909] log likelihood: -21901.084016
EM: Round [910] log likelihood: -21901.082763
EM: Round [911] log likelihood: -21901.081514
EM: Round [912] log likelihood: -21901.080267
EM: Round [913] log likelihood: -21901.079022
EM: Round [914] log likelihood: -21901.077779
EM: Round [915] log likelihood: -21901.076540
EM: Round [916] log likelihood: -21901.075302
EM: Round [917] log likelihood: -21901.074067
EM: Round [918] log likelihood: -21901.072834
EM: Round [919] log likelihood: -21901.071604
EM: Round [920] log likelihood: -21901.070376
EM: Round [921] log likelihood: -21901.069150
EM: Round [922] log likelihood: -21901.067927
EM: Round [923] log likelihood: -21901.066706
EM: Round [924] log likelihood: -21901.065487
EM: Round [925] log likelihood: -21901.064271
EM: Round [926] log likelihood: -21901.063057
EM: Round [927] log likelihood: -21901.061845
EM: Round [928] log likelihood: -21901.060636
EM: Round [929] log likelihood: -21901.059429
EM: Round [930] log likelihood: -21901.058225
EM: Round [931] log likelihood: -21901.057022
EM: Round [932] log likelihood: -21901.055822
EM: Round [933] log likelihood: -21901.054625
EM: Round [934] log likelihood: -21901.053430
EM: Round [935] log likelihood: -21901.052236
EM: Round [936] log likelihood: -21901.051046
EM: Round [937] log likelihood: -21901.049857
EM: Round [938] log likelihood: -21901.048671
EM: Round [939] log likelihood: -21901.047487
EM: Round [940] log likelihood: -21901.046306
EM: Round [941] log likelihood: -21901.045126
EM: Round [942] log likelihood: -21901.043949
EM: Round [943] log likelihood: -21901.042774
EM: Round [944] log likelihood: -21901.041602
EM: Round [945] log likelihood: -21901.040431
EM: Round [946] log likelihood: -21901.039263
EM: Round [947] log likelihood: -21901.038097
EM: Round [948] log likelihood: -21901.036933
EM: Round [949] log likelihood: -21901.035772
EM: Round [950] log likelihood: -21901.034613
EM: Round [951] log likelihood: -21901.033456
EM: Round [952] log likelihood: -21901.032301
EM: Round [953] log likelihood: -21901.031148
EM: Round [954] log likelihood: -21901.029998
EM: Round [955] log likelihood: -21901.028850
EM: Round [956] log likelihood: -21901.027704
EM: Round [957] log likelihood: -21901.026560
EM: Round [958] log likelihood: -21901.025418
EM: Round [959] log likelihood: -21901.024278
EM: Round [960] log likelihood: -21901.023141
EM: Round [961] log likelihood: -21901.022006
EM: Round [962] log likelihood: -21901.020873
EM: Round [963] log likelihood: -21901.019742
EM: Round [964] log likelihood: -21901.018613
EM: Round [965] log likelihood: -21901.017487
EM: Round [966] log likelihood: -21901.016362
EM: Round [967] log likelihood: -21901.015240
EM: Round [968] log likelihood: -21901.014120
EM: Round [969] log likelihood: -21901.013002
EM: Round [970] log likelihood: -21901.011886
EM: Round [971] log likelihood: -21901.010772
EM: Round [972] log likelihood: -21901.009660
EM: Round [973] log likelihood: -21901.008551
EM: Round [974] log likelihood: -21901.007443
EM: Round [975] log likelihood: -21901.006338
EM: Round [976] log likelihood: -21901.005234
EM: Round [977] log likelihood: -21901.004133
EM: Round [978] log likelihood: -21901.003034
EM: Round [979] log likelihood: -21901.001937
EM: Round [980] log likelihood: -21901.000842
EM: Round [981] log likelihood: -21900.999749
EM: Round [982] log likelihood: -21900.998658
EM: Round [983] log likelihood: -21900.997569
EM: Round [984] log likelihood: -21900.996482
EM: Round [985] log likelihood: -21900.995397
EM: Round [986] log likelihood: -21900.994315
EM: Round [987] log likelihood: -21900.993234
EM: Round [988] log likelihood: -21900.992155
EM: Round [989] log likelihood: -21900.991079
EM: Round [990] log likelihood: -21900.990004
EM: Round [991] log likelihood: -21900.988932
EM: Round [992] log likelihood: -21900.987861
EM: Round [993] log likelihood: -21900.986792
EM: Round [994] log likelihood: -21900.985726
EM: Round [995] log likelihood: -21900.984661
EM: Round [996] log likelihood: -21900.983599
EM: Round [997] log likelihood: -21900.982538
EM: Round [998] log likelihood: -21900.981480
EM: Round [999] log likelihood: -21900.980423
EM: Round [1000] log likelihood: -21900.979369
EM: Round [1001] log likelihood: -21900.978316
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir
-done, see /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -21223.674809
EM: Round [1] log likelihood: -21222.676840
EM: Round [2] log likelihood: -21222.631061
EM: Round [3] log likelihood: -21222.596451
EM: Round [4] log likelihood: -21222.567885
EM: Round [5] log likelihood: -21222.543016
EM: Round [6] log likelihood: -21222.520433
EM: Round [7] log likelihood: -21222.499284
EM: Round [8] log likelihood: -21222.479054
EM: Round [9] log likelihood: -21222.459435
EM: Round [10] log likelihood: -21222.440242
EM: Round [11] log likelihood: -21222.421361
EM: Round [12] log likelihood: -21222.402725
EM: Round [13] log likelihood: -21222.384294
EM: Round [14] log likelihood: -21222.366042
EM: Round [15] log likelihood: -21222.347952
EM: Round [16] log likelihood: -21222.330015
EM: Round [17] log likelihood: -21222.312224
EM: Round [18] log likelihood: -21222.294573
EM: Round [19] log likelihood: -21222.277060
EM: Round [20] log likelihood: -21222.259681
EM: Round [21] log likelihood: -21222.242433
EM: Round [22] log likelihood: -21222.225315
EM: Round [23] log likelihood: -21222.208325
EM: Round [24] log likelihood: -21222.191460
EM: Round [25] log likelihood: -21222.174719
EM: Round [26] log likelihood: -21222.158101
EM: Round [27] log likelihood: -21222.141602
EM: Round [28] log likelihood: -21222.125223
EM: Round [29] log likelihood: -21222.108960
EM: Round [30] log likelihood: -21222.092813
EM: Round [31] log likelihood: -21222.076780
EM: Round [32] log likelihood: -21222.060860
EM: Round [33] log likelihood: -21222.045051
EM: Round [34] log likelihood: -21222.029351
EM: Round [35] log likelihood: -21222.013760
EM: Round [36] log likelihood: -21221.998275
EM: Round [37] log likelihood: -21221.982896
EM: Round [38] log likelihood: -21221.967622
EM: Round [39] log likelihood: -21221.952450
EM: Round [40] log likelihood: -21221.937379
EM: Round [41] log likelihood: -21221.922409
EM: Round [42] log likelihood: -21221.907539
EM: Round [43] log likelihood: -21221.892766
EM: Round [44] log likelihood: -21221.878090
EM: Round [45] log likelihood: -21221.863509
EM: Round [46] log likelihood: -21221.849023
EM: Round [47] log likelihood: -21221.834630
EM: Round [48] log likelihood: -21221.820329
EM: Round [49] log likelihood: -21221.806120
EM: Round [50] log likelihood: -21221.792001
EM: Round [51] log likelihood: -21221.777970
EM: Round [52] log likelihood: -21221.764028
EM: Round [53] log likelihood: -21221.750173
EM: Round [54] log likelihood: -21221.736403
EM: Round [55] log likelihood: -21221.722719
EM: Round [56] log likelihood: -21221.709119
EM: Round [57] log likelihood: -21221.695602
EM: Round [58] log likelihood: -21221.682167
EM: Round [59] log likelihood: -21221.668814
EM: Round [60] log likelihood: -21221.655541
EM: Round [61] log likelihood: -21221.642347
EM: Round [62] log likelihood: -21221.629232
EM: Round [63] log likelihood: -21221.616196
EM: Round [64] log likelihood: -21221.603236
EM: Round [65] log likelihood: -21221.590352
EM: Round [66] log likelihood: -21221.577544
EM: Round [67] log likelihood: -21221.564810
EM: Round [68] log likelihood: -21221.552151
EM: Round [69] log likelihood: -21221.539564
EM: Round [70] log likelihood: -21221.527050
EM: Round [71] log likelihood: -21221.514607
EM: Round [72] log likelihood: -21221.502235
EM: Round [73] log likelihood: -21221.489933
EM: Round [74] log likelihood: -21221.477701
EM: Round [75] log likelihood: -21221.465537
EM: Round [76] log likelihood: -21221.453441
EM: Round [77] log likelihood: -21221.441413
EM: Round [78] log likelihood: -21221.429451
EM: Round [79] log likelihood: -21221.417556
EM: Round [80] log likelihood: -21221.405725
EM: Round [81] log likelihood: -21221.393960
EM: Round [82] log likelihood: -21221.382258
EM: Round [83] log likelihood: -21221.370621
EM: Round [84] log likelihood: -21221.359046
EM: Round [85] log likelihood: -21221.347533
EM: Round [86] log likelihood: -21221.336082
EM: Round [87] log likelihood: -21221.324692
EM: Round [88] log likelihood: -21221.313362
EM: Round [89] log likelihood: -21221.302093
EM: Round [90] log likelihood: -21221.290883
EM: Round [91] log likelihood: -21221.279732
EM: Round [92] log likelihood: -21221.268639
EM: Round [93] log likelihood: -21221.257604
EM: Round [94] log likelihood: -21221.246626
EM: Round [95] log likelihood: -21221.235705
EM: Round [96] log likelihood: -21221.224840
EM: Round [97] log likelihood: -21221.214031
EM: Round [98] log likelihood: -21221.203277
EM: Round [99] log likelihood: -21221.192578
EM: Round [100] log likelihood: -21221.181933
EM: Round [101] log likelihood: -21221.171342
EM: Round [102] log likelihood: -21221.160804
EM: Round [103] log likelihood: -21221.150319
EM: Round [104] log likelihood: -21221.139886
EM: Round [105] log likelihood: -21221.129506
EM: Round [106] log likelihood: -21221.119176
EM: Round [107] log likelihood: -21221.108898
EM: Round [108] log likelihood: -21221.098670
EM: Round [109] log likelihood: -21221.088493
EM: Round [110] log likelihood: -21221.078365
EM: Round [111] log likelihood: -21221.068286
EM: Round [112] log likelihood: -21221.058257
EM: Round [113] log likelihood: -21221.048275
EM: Round [114] log likelihood: -21221.038342
EM: Round [115] log likelihood: -21221.028457
EM: Round [116] log likelihood: -21221.018619
EM: Round [117] log likelihood: -21221.008828
EM: Round [118] log likelihood: -21220.999083
EM: Round [119] log likelihood: -21220.989384
EM: Round [120] log likelihood: -21220.979731
EM: Round [121] log likelihood: -21220.970124
EM: Round [122] log likelihood: -21220.960562
EM: Round [123] log likelihood: -21220.951044
EM: Round [124] log likelihood: -21220.941570
EM: Round [125] log likelihood: -21220.932141
EM: Round [126] log likelihood: -21220.922755
EM: Round [127] log likelihood: -21220.913413
EM: Round [128] log likelihood: -21220.904113
EM: Round [129] log likelihood: -21220.894856
EM: Round [130] log likelihood: -21220.885641
EM: Round [131] log likelihood: -21220.876468
EM: Round [132] log likelihood: -21220.867337
EM: Round [133] log likelihood: -21220.858247
EM: Round [134] log likelihood: -21220.849198
EM: Round [135] log likelihood: -21220.840189
EM: Round [136] log likelihood: -21220.831221
EM: Round [137] log likelihood: -21220.822293
EM: Round [138] log likelihood: -21220.813405
EM: Round [139] log likelihood: -21220.804556
EM: Round [140] log likelihood: -21220.795746
EM: Round [141] log likelihood: -21220.786976
EM: Round [142] log likelihood: -21220.778243
EM: Round [143] log likelihood: -21220.769549
EM: Round [144] log likelihood: -21220.760893
EM: Round [145] log likelihood: -21220.752275
EM: Round [146] log likelihood: -21220.743694
EM: Round [147] log likelihood: -21220.735151
EM: Round [148] log likelihood: -21220.726644
EM: Round [149] log likelihood: -21220.718174
EM: Round [150] log likelihood: -21220.709740
EM: Round [151] log likelihood: -21220.701342
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EM: Round [613] log likelihood: -21218.720085
EM: Round [614] log likelihood: -21218.717902
EM: Round [615] log likelihood: -21218.715724
EM: Round [616] log likelihood: -21218.713550
EM: Round [617] log likelihood: -21218.711382
EM: Round [618] log likelihood: -21218.709218
EM: Round [619] log likelihood: -21218.707059
EM: Round [620] log likelihood: -21218.704905
EM: Round [621] log likelihood: -21218.702755
EM: Round [622] log likelihood: -21218.700610
EM: Round [623] log likelihood: -21218.698470
EM: Round [624] log likelihood: -21218.696335
EM: Round [625] log likelihood: -21218.694204
EM: Round [626] log likelihood: -21218.692078
EM: Round [627] log likelihood: -21218.689957
EM: Round [628] log likelihood: -21218.687840
EM: Round [629] log likelihood: -21218.685728
EM: Round [630] log likelihood: -21218.683621
EM: Round [631] log likelihood: -21218.681518
EM: Round [632] log likelihood: -21218.679420
EM: Round [633] log likelihood: -21218.677326
EM: Round [634] log likelihood: -21218.675237
EM: Round [635] log likelihood: -21218.673153
EM: Round [636] log likelihood: -21218.671073
EM: Round [637] log likelihood: -21218.668998
EM: Round [638] log likelihood: -21218.666927
EM: Round [639] log likelihood: -21218.664861
EM: Round [640] log likelihood: -21218.662799
EM: Round [641] log likelihood: -21218.660742
EM: Round [642] log likelihood: -21218.658689
EM: Round [643] log likelihood: -21218.656641
EM: Round [644] log likelihood: -21218.654597
EM: Round [645] log likelihood: -21218.652557
EM: Round [646] log likelihood: -21218.650522
EM: Round [647] log likelihood: -21218.648492
EM: Round [648] log likelihood: -21218.646466
EM: Round [649] log likelihood: -21218.644444
EM: Round [650] log likelihood: -21218.642426
EM: Round [651] log likelihood: -21218.640413
EM: Round [652] log likelihood: -21218.638404
EM: Round [653] log likelihood: -21218.636400
EM: Round [654] log likelihood: -21218.634400
EM: Round [655] log likelihood: -21218.632404
EM: Round [656] log likelihood: -21218.630413
EM: Round [657] log likelihood: -21218.628426
EM: Round [658] log likelihood: -21218.626443
EM: Round [659] log likelihood: -21218.624464
EM: Round [660] log likelihood: -21218.622490
EM: Round [661] log likelihood: -21218.620520
EM: Round [662] log likelihood: -21218.618554
EM: Round [663] log likelihood: -21218.616592
EM: Round [664] log likelihood: -21218.614635
EM: Round [665] log likelihood: -21218.612681
EM: Round [666] log likelihood: -21218.610732
EM: Round [667] log likelihood: -21218.608787
EM: Round [668] log likelihood: -21218.606847
EM: Round [669] log likelihood: -21218.604910
EM: Round [670] log likelihood: -21218.602977
EM: Round [671] log likelihood: -21218.601049
EM: Round [672] log likelihood: -21218.599125
EM: Round [673] log likelihood: -21218.597205
EM: Round [674] log likelihood: -21218.595289
EM: Round [675] log likelihood: -21218.593377
EM: Round [676] log likelihood: -21218.591469
EM: Round [677] log likelihood: -21218.589565
EM: Round [678] log likelihood: -21218.587665
EM: Round [679] log likelihood: -21218.585769
EM: Round [680] log likelihood: -21218.583878
EM: Round [681] log likelihood: -21218.581990
EM: Round [682] log likelihood: -21218.580106
EM: Round [683] log likelihood: -21218.578227
EM: Round [684] log likelihood: -21218.576351
EM: Round [685] log likelihood: -21218.574479
EM: Round [686] log likelihood: -21218.572611
EM: Round [687] log likelihood: -21218.570747
EM: Round [688] log likelihood: -21218.568888
EM: Round [689] log likelihood: -21218.567032
EM: Round [690] log likelihood: -21218.565179
EM: Round [691] log likelihood: -21218.563331
EM: Round [692] log likelihood: -21218.561487
EM: Round [693] log likelihood: -21218.559647
EM: Round [694] log likelihood: -21218.557810
EM: Round [695] log likelihood: -21218.555977
EM: Round [696] log likelihood: -21218.554149
EM: Round [697] log likelihood: -21218.552324
EM: Round [698] log likelihood: -21218.550503
EM: Round [699] log likelihood: -21218.548685
EM: Round [700] log likelihood: -21218.546872
EM: Round [701] log likelihood: -21218.545062
EM: Round [702] log likelihood: -21218.543256
EM: Round [703] log likelihood: -21218.541454
EM: Round [704] log likelihood: -21218.539656
EM: Round [705] log likelihood: -21218.537861
EM: Round [706] log likelihood: -21218.536070
EM: Round [707] log likelihood: -21218.534283
EM: Round [708] log likelihood: -21218.532500
EM: Round [709] log likelihood: -21218.530720
EM: Round [710] log likelihood: -21218.528944
EM: Round [711] log likelihood: -21218.527172
EM: Round [712] log likelihood: -21218.525403
EM: Round [713] log likelihood: -21218.523639
EM: Round [714] log likelihood: -21218.521877
EM: Round [715] log likelihood: -21218.520120
EM: Round [716] log likelihood: -21218.518366
EM: Round [717] log likelihood: -21218.516616
EM: Round [718] log likelihood: -21218.514869
EM: Round [719] log likelihood: -21218.513126
EM: Round [720] log likelihood: -21218.511387
EM: Round [721] log likelihood: -21218.509651
EM: Round [722] log likelihood: -21218.507919
EM: Round [723] log likelihood: -21218.506190
EM: Round [724] log likelihood: -21218.504465
EM: Round [725] log likelihood: -21218.502744
EM: Round [726] log likelihood: -21218.501026
EM: Round [727] log likelihood: -21218.499312
EM: Round [728] log likelihood: -21218.497601
EM: Round [729] log likelihood: -21218.495893
EM: Round [730] log likelihood: -21218.494190
EM: Round [731] log likelihood: -21218.492490
EM: Round [732] log likelihood: -21218.490793
EM: Round [733] log likelihood: -21218.489100
EM: Round [734] log likelihood: -21218.487410
EM: Round [735] log likelihood: -21218.485723
EM: Round [736] log likelihood: -21218.484041
EM: Round [737] log likelihood: -21218.482361
EM: Round [738] log likelihood: -21218.480685
EM: Round [739] log likelihood: -21218.479013
EM: Round [740] log likelihood: -21218.477344
EM: Round [741] log likelihood: -21218.475678
EM: Round [742] log likelihood: -21218.474016
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EM: Round [744] log likelihood: -21218.470702
EM: Round [745] log likelihood: -21218.469050
EM: Round [746] log likelihood: -21218.467401
EM: Round [747] log likelihood: -21218.465756
EM: Round [748] log likelihood: -21218.464114
EM: Round [749] log likelihood: -21218.462475
EM: Round [750] log likelihood: -21218.460840
EM: Round [751] log likelihood: -21218.459208
EM: Round [752] log likelihood: -21218.457579
EM: Round [753] log likelihood: -21218.455954
EM: Round [754] log likelihood: -21218.454332
EM: Round [755] log likelihood: -21218.452713
EM: Round [756] log likelihood: -21218.451098
EM: Round [757] log likelihood: -21218.449486
EM: Round [758] log likelihood: -21218.447877
EM: Round [759] log likelihood: -21218.446271
EM: Round [760] log likelihood: -21218.444669
EM: Round [761] log likelihood: -21218.443070
EM: Round [762] log likelihood: -21218.441474
EM: Round [763] log likelihood: -21218.439882
EM: Round [764] log likelihood: -21218.438292
EM: Round [765] log likelihood: -21218.436706
EM: Round [766] log likelihood: -21218.435123
EM: Round [767] log likelihood: -21218.433543
EM: Round [768] log likelihood: -21218.431967
EM: Round [769] log likelihood: -21218.430393
EM: Round [770] log likelihood: -21218.428823
EM: Round [771] log likelihood: -21218.427256
EM: Round [772] log likelihood: -21218.425692
EM: Round [773] log likelihood: -21218.424132
EM: Round [774] log likelihood: -21218.422574
EM: Round [775] log likelihood: -21218.421020
EM: Round [776] log likelihood: -21218.419468
EM: Round [777] log likelihood: -21218.417920
EM: Round [778] log likelihood: -21218.416375
EM: Round [779] log likelihood: -21218.414833
EM: Round [780] log likelihood: -21218.413294
EM: Round [781] log likelihood: -21218.411758
EM: Round [782] log likelihood: -21218.410226
EM: Round [783] log likelihood: -21218.408696
EM: Round [784] log likelihood: -21218.407169
EM: Round [785] log likelihood: -21218.405646
EM: Round [786] log likelihood: -21218.404125
EM: Round [787] log likelihood: -21218.402608
EM: Round [788] log likelihood: -21218.401093
EM: Round [789] log likelihood: -21218.399582
EM: Round [790] log likelihood: -21218.398074
EM: Round [791] log likelihood: -21218.396568
EM: Round [792] log likelihood: -21218.395066
EM: Round [793] log likelihood: -21218.393567
EM: Round [794] log likelihood: -21218.392070
EM: Round [795] log likelihood: -21218.390577
EM: Round [796] log likelihood: -21218.389086
EM: Round [797] log likelihood: -21218.387599
EM: Round [798] log likelihood: -21218.386114
EM: Round [799] log likelihood: -21218.384633
EM: Round [800] log likelihood: -21218.383154
EM: Round [801] log likelihood: -21218.381679
EM: Round [802] log likelihood: -21218.380206
EM: Round [803] log likelihood: -21218.378736
EM: Round [804] log likelihood: -21218.377269
EM: Round [805] log likelihood: -21218.375805
EM: Round [806] log likelihood: -21218.374344
EM: Round [807] log likelihood: -21218.372886
EM: Round [808] log likelihood: -21218.371431
EM: Round [809] log likelihood: -21218.369978
EM: Round [810] log likelihood: -21218.368529
EM: Round [811] log likelihood: -21218.367082
EM: Round [812] log likelihood: -21218.365638
EM: Round [813] log likelihood: -21218.364197
EM: Round [814] log likelihood: -21218.362759
EM: Round [815] log likelihood: -21218.361324
EM: Round [816] log likelihood: -21218.359891
EM: Round [817] log likelihood: -21218.358462
EM: Round [818] log likelihood: -21218.357035
EM: Round [819] log likelihood: -21218.355611
EM: Round [820] log likelihood: -21218.354190
EM: Round [821] log likelihood: -21218.352771
EM: Round [822] log likelihood: -21218.351356
EM: Round [823] log likelihood: -21218.349943
EM: Round [824] log likelihood: -21218.348533
EM: Round [825] log likelihood: -21218.347125
EM: Round [826] log likelihood: -21218.345721
EM: Round [827] log likelihood: -21218.344319
EM: Round [828] log likelihood: -21218.342920
EM: Round [829] log likelihood: -21218.341524
EM: Round [830] log likelihood: -21218.340130
EM: Round [831] log likelihood: -21218.338739
EM: Round [832] log likelihood: -21218.337351
EM: Round [833] log likelihood: -21218.335966
EM: Round [834] log likelihood: -21218.334583
EM: Round [835] log likelihood: -21218.333203
EM: Round [836] log likelihood: -21218.331826
EM: Round [837] log likelihood: -21218.330451
EM: Round [838] log likelihood: -21218.329079
EM: Round [839] log likelihood: -21218.327710
EM: Round [840] log likelihood: -21218.326344
EM: Round [841] log likelihood: -21218.324980
EM: Round [842] log likelihood: -21218.323618
EM: Round [843] log likelihood: -21218.322260
EM: Round [844] log likelihood: -21218.320904
EM: Round [845] log likelihood: -21218.319551
EM: Round [846] log likelihood: -21218.318200
EM: Round [847] log likelihood: -21218.316852
EM: Round [848] log likelihood: -21218.315506
EM: Round [849] log likelihood: -21218.314164
EM: Round [850] log likelihood: -21218.312823
EM: Round [851] log likelihood: -21218.311486
EM: Round [852] log likelihood: -21218.310151
EM: Round [853] log likelihood: -21218.308818
EM: Round [854] log likelihood: -21218.307489
EM: Round [855] log likelihood: -21218.306161
EM: Round [856] log likelihood: -21218.304837
EM: Round [857] log likelihood: -21218.303514
EM: Round [858] log likelihood: -21218.302195
EM: Round [859] log likelihood: -21218.300878
EM: Round [860] log likelihood: -21218.299563
EM: Round [861] log likelihood: -21218.298251
EM: Round [862] log likelihood: -21218.296942
EM: Round [863] log likelihood: -21218.295635
EM: Round [864] log likelihood: -21218.294331
EM: Round [865] log likelihood: -21218.293029
EM: Round [866] log likelihood: -21218.291730
EM: Round [867] log likelihood: -21218.290433
EM: Round [868] log likelihood: -21218.289138
EM: Round [869] log likelihood: -21218.287847
EM: Round [870] log likelihood: -21218.286557
EM: Round [871] log likelihood: -21218.285270
EM: Round [872] log likelihood: -21218.283986
EM: Round [873] log likelihood: -21218.282704
EM: Round [874] log likelihood: -21218.281425
EM: Round [875] log likelihood: -21218.280148
EM: Round [876] log likelihood: -21218.278873
EM: Round [877] log likelihood: -21218.277601
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EM: Round [880] log likelihood: -21218.273799
EM: Round [881] log likelihood: -21218.272537
EM: Round [882] log likelihood: -21218.271277
EM: Round [883] log likelihood: -21218.270019
EM: Round [884] log likelihood: -21218.268764
EM: Round [885] log likelihood: -21218.267511
EM: Round [886] log likelihood: -21218.266261
EM: Round [887] log likelihood: -21218.265013
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EM: Round [889] log likelihood: -21218.262524
EM: Round [890] log likelihood: -21218.261283
EM: Round [891] log likelihood: -21218.260045
EM: Round [892] log likelihood: -21218.258809
EM: Round [893] log likelihood: -21218.257575
EM: Round [894] log likelihood: -21218.256344
EM: Round [895] log likelihood: -21218.255115
EM: Round [896] log likelihood: -21218.253888
EM: Round [897] log likelihood: -21218.252663
EM: Round [898] log likelihood: -21218.251441
EM: Round [899] log likelihood: -21218.250222
EM: Round [900] log likelihood: -21218.249004
EM: Round [901] log likelihood: -21218.247789
EM: Round [902] log likelihood: -21218.246576
EM: Round [903] log likelihood: -21218.245366
EM: Round [904] log likelihood: -21218.244158
EM: Round [905] log likelihood: -21218.242952
EM: Round [906] log likelihood: -21218.241748
EM: Round [907] log likelihood: -21218.240547
EM: Round [908] log likelihood: -21218.239348
EM: Round [909] log likelihood: -21218.238151
EM: Round [910] log likelihood: -21218.236956
EM: Round [911] log likelihood: -21218.235764
EM: Round [912] log likelihood: -21218.234574
EM: Round [913] log likelihood: -21218.233386
EM: Round [914] log likelihood: -21218.232201
EM: Round [915] log likelihood: -21218.231018
EM: Round [916] log likelihood: -21218.229837
EM: Round [917] log likelihood: -21218.228658
EM: Round [918] log likelihood: -21218.227481
EM: Round [919] log likelihood: -21218.226307
EM: Round [920] log likelihood: -21218.225135
EM: Round [921] log likelihood: -21218.223965
EM: Round [922] log likelihood: -21218.222797
EM: Round [923] log likelihood: -21218.221631
EM: Round [924] log likelihood: -21218.220468
EM: Round [925] log likelihood: -21218.219307
EM: Round [926] log likelihood: -21218.218148
EM: Round [927] log likelihood: -21218.216991
EM: Round [928] log likelihood: -21218.215836
EM: Round [929] log likelihood: -21218.214684
EM: Round [930] log likelihood: -21218.213534
EM: Round [931] log likelihood: -21218.212386
EM: Round [932] log likelihood: -21218.211240
EM: Round [933] log likelihood: -21218.210096
EM: Round [934] log likelihood: -21218.208954
EM: Round [935] log likelihood: -21218.207814
EM: Round [936] log likelihood: -21218.206677
EM: Round [937] log likelihood: -21218.205542
EM: Round [938] log likelihood: -21218.204409
EM: Round [939] log likelihood: -21218.203278
EM: Round [940] log likelihood: -21218.202149
EM: Round [941] log likelihood: -21218.201022
EM: Round [942] log likelihood: -21218.199897
EM: Round [943] log likelihood: -21218.198774
EM: Round [944] log likelihood: -21218.197654
EM: Round [945] log likelihood: -21218.196536
EM: Round [946] log likelihood: -21218.195419
EM: Round [947] log likelihood: -21218.194305
EM: Round [948] log likelihood: -21218.193193
EM: Round [949] log likelihood: -21218.192083
EM: Round [950] log likelihood: -21218.190975
EM: Round [951] log likelihood: -21218.189869
EM: Round [952] log likelihood: -21218.188765
EM: Round [953] log likelihood: -21218.187663
EM: Round [954] log likelihood: -21218.186563
EM: Round [955] log likelihood: -21218.185465
EM: Round [956] log likelihood: -21218.184370
EM: Round [957] log likelihood: -21218.183276
EM: Round [958] log likelihood: -21218.182184
EM: Round [959] log likelihood: -21218.181095
EM: Round [960] log likelihood: -21218.180007
EM: Round [961] log likelihood: -21218.178922
EM: Round [962] log likelihood: -21218.177838
EM: Round [963] log likelihood: -21218.176756
EM: Round [964] log likelihood: -21218.175677
EM: Round [965] log likelihood: -21218.174599
EM: Round [966] log likelihood: -21218.173524
EM: Round [967] log likelihood: -21218.172450
EM: Round [968] log likelihood: -21218.171379
EM: Round [969] log likelihood: -21218.170309
EM: Round [970] log likelihood: -21218.169241
EM: Round [971] log likelihood: -21218.168176
EM: Round [972] log likelihood: -21218.167112
EM: Round [973] log likelihood: -21218.166050
EM: Round [974] log likelihood: -21218.164991
EM: Round [975] log likelihood: -21218.163933
EM: Round [976] log likelihood: -21218.162877
EM: Round [977] log likelihood: -21218.161823
EM: Round [978] log likelihood: -21218.160771
EM: Round [979] log likelihood: -21218.159721
EM: Round [980] log likelihood: -21218.158673
EM: Round [981] log likelihood: -21218.157627
EM: Round [982] log likelihood: -21218.156583
EM: Round [983] log likelihood: -21218.155541
EM: Round [984] log likelihood: -21218.154500
EM: Round [985] log likelihood: -21218.153462
EM: Round [986] log likelihood: -21218.152425
EM: Round [987] log likelihood: -21218.151390
EM: Round [988] log likelihood: -21218.150358
EM: Round [989] log likelihood: -21218.149327
EM: Round [990] log likelihood: -21218.148298
EM: Round [991] log likelihood: -21218.147271
EM: Round [992] log likelihood: -21218.146246
EM: Round [993] log likelihood: -21218.145222
EM: Round [994] log likelihood: -21218.144201
EM: Round [995] log likelihood: -21218.143181
EM: Round [996] log likelihood: -21218.142164
EM: Round [997] log likelihood: -21218.141148
EM: Round [998] log likelihood: -21218.140134
EM: Round [999] log likelihood: -21218.139122
EM: Round [1000] log likelihood: -21218.138112
EM: Round [1001] log likelihood: -21218.137103
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294765771
Execution Time = 5.95 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.e487RzRTjW/fi_workdir/microH.dat
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.e487RzRTjW/fi_workdir/microH.dat /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.e487RzRTjW/fi_workdir/microH.dat /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.e487RzRTjW --json_outfile /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.e487RzRTjW --json_outfile /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1
Running: touch /tmp/nxf.e487RzRTjW/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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000230534.6]
WARNING, no entry stored in dbm for [ENSG00000216829.6]
WARNING, no entry stored in dbm for [ENSG00000216829.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
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 [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000236031.1]
WARNING, no entry stored in dbm for [ENSG00000236197.4]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.e487RzRTjW/ctat_genome_lib_build_dir > /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.e487RzRTjW/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory