Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2f1ab7db80a50194505cda6a54a440/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/7dbee5c6f334ab661e3c02c0267dc0/.command.sh
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/f4/7dbee5c6f334ab661e3c02c0267dc0/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2f1ab7db80a50194505cda6a54a440/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/bb1e2d64c50b7674419b4fcdbad69a/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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_23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/cytoBand.txt
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed
-parsing GTF file: /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star --out_dir /tmp/nxf.b9RdbAI3hE/fi_workdir --reads "/tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:30:49 ..... started STAR run
Jun 08 10:30:49 ..... loading genome
Jun 08 10:32:32 ... generating Suffix Array index
Jun 08 10:36:12 ... completed Suffix Array index
Jun 08 10:36:12 ..... processing annotations GTF
Jun 08 10:36:12 ..... inserting junctions into the genome indices
Jun 08 10:37:13 ..... started mapping
Jun 08 11:28:13 ..... finished mapping
Jun 08 11:28:14 ..... started sorting BAM
Jun 08 11:28:16 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam
Execution Time = 57.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star --out_dir /tmp/nxf.b9RdbAI3hE/fi_workdir --reads "/tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:28:38 : INFO : Done.
Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf
-parsing /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam
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[3420000] -done parsing /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21,
'per_id < 96' => 23149,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 60,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 272,
'seq-similar region overlap' => 214,
'exons hit < 2' => 6,
'num genes matched < 2' => 33,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 12,
'excessive soft clipping' => 26406,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 46,
'low complexity anchor region' => 20,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
' ** passed ** ' => 45164,
'small anchor length' => 315
};
-writing fusion junction support info.
Execution Time = 1.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[3000] -fusion SPANNING read extraction for scaff: AC005050.1--SLC26A3
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[20000] -fusion SPANNING read extraction for scaff: AC092142.1--ELAPOR2
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[58000] -fusion SPANNING read extraction for scaff: AL033504.1--SASH1
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[204000] -fusion SPANNING read extraction for scaff: BIRC6--ITGA9
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[23000] -fusion SPANNING read extraction for scaff: CENPP--ASZ1
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[23000] -fusion SPANNING read extraction for scaff: CHST11--SYK
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[17000] -fusion SPANNING read extraction for scaff: CHST11--DIRAS2
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[17000] -fusion SPANNING read extraction for scaff: CHST11--OR7E109P
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[101000] -fusion SPANNING read extraction for scaff: CLASP1--NRCAM
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[38000] -fusion SPANNING read extraction for scaff: COBL--LINC01866
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[38000] -fusion SPANNING read extraction for scaff: COBL--RN7SKP168
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[40000] -fusion SPANNING read extraction for scaff: COL13A1--SPON1
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[62000] -fusion SPANNING read extraction for scaff: DGCR2--WARS2-AS1
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[58000] -fusion SPANNING read extraction for scaff: EPHB2--TMEM39B
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[54000] -fusion SPANNING read extraction for scaff: FAF1--CDKN2C
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[36000] -fusion SPANNING read extraction for scaff: FAF1--MIR4421
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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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[119000] -fusion SPANNING read extraction for scaff: GTF2H2--FAM114A1
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[150000] -fusion SPANNING read extraction for scaff: HMGA2--CHMP1A
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[14000] -fusion SPANNING read extraction for scaff: LPAR1--SUSD1
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[77000] -fusion SPANNING read extraction for scaff: MFSD14B--LINC01591
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[133000] -fusion SPANNING read extraction for scaff: MMP24OS--PTPRT
-fusion SPANNING read extraction for scaff: NTM-AS1--OPCML
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[122000] -fusion SPANNING read extraction for scaff: NUP98--PRMT3
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[56000] -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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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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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--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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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--PCDHGB6
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[82000] -fusion SPANNING read extraction for scaff: POLR2J3--KIF16B
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[53000] -fusion SPANNING read extraction for scaff: PSMB2--CELF4
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[180000] -fusion SPANNING read extraction for scaff: PXN--PLA2G1B
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[12000] -fusion SPANNING read extraction for scaff: SDHAF3--AC025614.2
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[12000] -fusion SPANNING read extraction for scaff: SDHAF3--LINC01985
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[13000] -fusion SPANNING read extraction for scaff: SLC30A7--UROC1
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[210000] -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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[52000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[127000] -fusion SPANNING read extraction for scaff: ST7--AC006001.3
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[17000] -fusion SPANNING read extraction for scaff: TENT4B--AF254982.1
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[17000] -fusion SPANNING read extraction for scaff: TENT4B--AP001464.1
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[51000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[28000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[66000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[118000] -fusion SPANNING read extraction for scaff: UHRF2--SLC1A1
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[157000] -fusion SPANNING read extraction for scaff: XYLB--GOLGA4
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[83000] -fusion SPANNING read extraction for scaff: ZBTB40--ZMYM4
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[38000] -fusion SPANNING read extraction for scaff: ZFP62--SIMC1
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[15000] -fusion SPANNING read extraction for scaff: ZNF559--ZNF177
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 27491,
'lacks exon overlap' => 174764
};
Execution Time = 4.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -20978.211364
EM: Round [1] log likelihood: -20970.110148
EM: Round [2] log likelihood: -20968.416238
EM: Round [3] log likelihood: -20967.049984
EM: Round [4] log likelihood: -20965.936952
EM: Round [5] log likelihood: -20965.024101
EM: Round [6] log likelihood: -20964.270527
EM: Round [7] log likelihood: -20963.644411
EM: Round [8] log likelihood: -20963.120815
EM: Round [9] log likelihood: -20962.680076
EM: Round [10] log likelihood: -20962.306607
EM: Round [11] log likelihood: -20961.987992
EM: Round [12] log likelihood: -20961.714298
EM: Round [13] log likelihood: -20961.477545
EM: Round [14] log likelihood: -20961.271301
EM: Round [15] log likelihood: -20961.090358
EM: Round [16] log likelihood: -20960.930485
EM: Round [17] log likelihood: -20960.788233
EM: Round [18] log likelihood: -20960.660780
EM: Round [19] log likelihood: -20960.545808
EM: Round [20] log likelihood: -20960.441407
EM: Round [21] log likelihood: -20960.345996
EM: Round [22] log likelihood: -20960.258264
EM: Round [23] log likelihood: -20960.177116
EM: Round [24] log likelihood: -20960.101639
EM: Round [25] log likelihood: -20960.031066
EM: Round [26] log likelihood: -20959.964750
EM: Round [27] log likelihood: -20959.902145
EM: Round [28] log likelihood: -20959.842788
EM: Round [29] log likelihood: -20959.786285
EM: Round [30] log likelihood: -20959.732301
EM: Round [31] log likelihood: -20959.680547
EM: Round [32] log likelihood: -20959.630777
EM: Round [33] log likelihood: -20959.582778
EM: Round [34] log likelihood: -20959.536366
EM: Round [35] log likelihood: -20959.491383
EM: Round [36] log likelihood: -20959.447691
EM: Round [37] log likelihood: -20959.405169
EM: Round [38] log likelihood: -20959.363712
EM: Round [39] log likelihood: -20959.323231
EM: Round [40] log likelihood: -20959.283643
EM: Round [41] log likelihood: -20959.244880
EM: Round [42] log likelihood: -20959.206878
EM: Round [43] log likelihood: -20959.169583
EM: Round [44] log likelihood: -20959.132948
EM: Round [45] log likelihood: -20959.096928
EM: Round [46] log likelihood: -20959.061487
EM: Round [47] log likelihood: -20959.026589
EM: Round [48] log likelihood: -20958.992206
EM: Round [49] log likelihood: -20958.958309
EM: Round [50] log likelihood: -20958.924875
EM: Round [51] log likelihood: -20958.891882
EM: Round [52] log likelihood: -20958.859310
EM: Round [53] log likelihood: -20958.827141
EM: Round [54] log likelihood: -20958.795360
EM: Round [55] log likelihood: -20958.763951
EM: Round [56] log likelihood: -20958.732901
EM: Round [57] log likelihood: -20958.702198
EM: Round [58] log likelihood: -20958.671831
EM: Round [59] log likelihood: -20958.641790
EM: Round [60] log likelihood: -20958.612064
EM: Round [61] log likelihood: -20958.582646
EM: Round [62] log likelihood: -20958.553526
EM: Round [63] log likelihood: -20958.524698
EM: Round [64] log likelihood: -20958.496154
EM: Round [65] log likelihood: -20958.467887
EM: Round [66] log likelihood: -20958.439892
EM: Round [67] log likelihood: -20958.412162
EM: Round [68] log likelihood: -20958.384691
EM: Round [69] log likelihood: -20958.357475
EM: Round [70] log likelihood: -20958.330508
EM: Round [71] log likelihood: -20958.303786
EM: Round [72] log likelihood: -20958.277304
EM: Round [73] log likelihood: -20958.251058
EM: Round [74] log likelihood: -20958.225043
EM: Round [75] log likelihood: -20958.199255
EM: Round [76] log likelihood: -20958.173691
EM: Round [77] log likelihood: -20958.148347
EM: Round [78] log likelihood: -20958.123219
EM: Round [79] log likelihood: -20958.098303
EM: Round [80] log likelihood: -20958.073597
EM: Round [81] log likelihood: -20958.049098
EM: Round [82] log likelihood: -20958.024801
EM: Round [83] log likelihood: -20958.000704
EM: Round [84] log likelihood: -20957.976804
EM: Round [85] log likelihood: -20957.953098
EM: Round [86] log likelihood: -20957.929583
EM: Round [87] log likelihood: -20957.906257
EM: Round [88] log likelihood: -20957.883116
EM: Round [89] log likelihood: -20957.860159
EM: Round [90] log likelihood: -20957.837382
EM: Round [91] log likelihood: -20957.814784
EM: Round [92] log likelihood: -20957.792361
EM: Round [93] log likelihood: -20957.770112
EM: Round [94] log likelihood: -20957.748033
EM: Round [95] log likelihood: -20957.726123
EM: Round [96] log likelihood: -20957.704380
EM: Round [97] log likelihood: -20957.682801
EM: Round [98] log likelihood: -20957.661384
EM: Round [99] log likelihood: -20957.640128
EM: Round [100] log likelihood: -20957.619029
EM: Round [101] log likelihood: -20957.598086
EM: Round [102] log likelihood: -20957.577298
EM: Round [103] log likelihood: -20957.556661
EM: Round [104] log likelihood: -20957.536175
EM: Round [105] log likelihood: -20957.515838
EM: Round [106] log likelihood: -20957.495646
EM: Round [107] log likelihood: -20957.475600
EM: Round [108] log likelihood: -20957.455697
EM: Round [109] log likelihood: -20957.435935
EM: Round [110] log likelihood: -20957.416312
EM: Round [111] log likelihood: -20957.396828
EM: Round [112] log likelihood: -20957.377480
EM: Round [113] log likelihood: -20957.358266
EM: Round [114] log likelihood: -20957.339186
EM: Round [115] log likelihood: -20957.320237
EM: Round [116] log likelihood: -20957.301419
EM: Round [117] log likelihood: -20957.282729
EM: Round [118] log likelihood: -20957.264166
EM: Round [119] log likelihood: -20957.245729
EM: Round [120] log likelihood: -20957.227416
EM: Round [121] log likelihood: -20957.209226
EM: Round [122] log likelihood: -20957.191157
EM: Round [123] log likelihood: -20957.173209
EM: Round [124] log likelihood: -20957.155379
EM: Round [125] log likelihood: -20957.137667
EM: Round [126] log likelihood: -20957.120071
EM: Round [127] log likelihood: -20957.102591
EM: Round [128] log likelihood: -20957.085223
EM: Round [129] log likelihood: -20957.067969
EM: Round [130] log likelihood: -20957.050825
EM: Round [131] log likelihood: -20957.033792
EM: Round [132] log likelihood: -20957.016868
EM: Round [133] log likelihood: -20957.000052
EM: Round [134] log likelihood: -20956.983342
EM: Round [135] log likelihood: -20956.966738
EM: Round [136] log likelihood: -20956.950238
EM: Round [137] log likelihood: -20956.933842
EM: Round [138] log likelihood: -20956.917548
EM: Round [139] log likelihood: -20956.901355
EM: Round [140] log likelihood: -20956.885262
EM: Round [141] log likelihood: -20956.869269
EM: Round [142] log likelihood: -20956.853374
EM: Round [143] log likelihood: -20956.837577
EM: Round [144] log likelihood: -20956.821875
EM: Round [145] log likelihood: -20956.806269
EM: Round [146] log likelihood: -20956.790757
EM: Round [147] log likelihood: -20956.775339
EM: Round [148] log likelihood: -20956.760014
EM: Round [149] log likelihood: -20956.744780
EM: Round [150] log likelihood: -20956.729636
EM: Round [151] log likelihood: -20956.714583
EM: Round [152] log likelihood: -20956.699619
EM: Round [153] log likelihood: -20956.684743
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Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam into /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir
-done, see /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -20205.185293
EM: Round [1] log likelihood: -20204.696221
EM: Round [2] log likelihood: -20204.661028
EM: Round [3] log likelihood: -20204.626667
EM: Round [4] log likelihood: -20204.592730
EM: Round [5] log likelihood: -20204.559205
EM: Round [6] log likelihood: -20204.526082
EM: Round [7] log likelihood: -20204.493354
EM: Round [8] log likelihood: -20204.461010
EM: Round [9] log likelihood: -20204.429044
EM: Round [10] log likelihood: -20204.397446
EM: Round [11] log likelihood: -20204.366209
EM: Round [12] log likelihood: -20204.335325
EM: Round [13] log likelihood: -20204.304787
EM: Round [14] log likelihood: -20204.274588
EM: Round [15] log likelihood: -20204.244720
EM: Round [16] log likelihood: -20204.215178
EM: Round [17] log likelihood: -20204.185955
EM: Round [18] log likelihood: -20204.157044
EM: Round [19] log likelihood: -20204.128439
EM: Round [20] log likelihood: -20204.100135
EM: Round [21] log likelihood: -20204.072126
EM: Round [22] log likelihood: -20204.044405
EM: Round [23] log likelihood: -20204.016968
EM: Round [24] log likelihood: -20203.989809
EM: Round [25] log likelihood: -20203.962924
EM: Round [26] log likelihood: -20203.936307
EM: Round [27] log likelihood: -20203.909953
EM: Round [28] log likelihood: -20203.883858
EM: Round [29] log likelihood: -20203.858016
EM: Round [30] log likelihood: -20203.832425
EM: Round [31] log likelihood: -20203.807078
EM: Round [32] log likelihood: -20203.781973
EM: Round [33] log likelihood: -20203.757104
EM: Round [34] log likelihood: -20203.732469
EM: Round [35] log likelihood: -20203.708062
EM: Round [36] log likelihood: -20203.683880
EM: Round [37] log likelihood: -20203.659919
EM: Round [38] log likelihood: -20203.636177
EM: Round [39] log likelihood: -20203.612648
EM: Round [40] log likelihood: -20203.589330
EM: Round [41] log likelihood: -20203.566220
EM: Round [42] log likelihood: -20203.543313
EM: Round [43] log likelihood: -20203.520607
EM: Round [44] log likelihood: -20203.498099
EM: Round [45] log likelihood: -20203.475786
EM: Round [46] log likelihood: -20203.453664
EM: Round [47] log likelihood: -20203.431731
EM: Round [48] log likelihood: -20203.409984
EM: Round [49] log likelihood: -20203.388420
EM: Round [50] log likelihood: -20203.367036
EM: Round [51] log likelihood: -20203.345830
EM: Round [52] log likelihood: -20203.324799
EM: Round [53] log likelihood: -20203.303940
EM: Round [54] log likelihood: -20203.283252
EM: Round [55] log likelihood: -20203.262731
EM: Round [56] log likelihood: -20203.242375
EM: Round [57] log likelihood: -20203.222182
EM: Round [58] log likelihood: -20203.202150
EM: Round [59] log likelihood: -20203.182276
EM: Round [60] log likelihood: -20203.162558
EM: Round [61] log likelihood: -20203.142994
EM: Round [62] log likelihood: -20203.123581
EM: Round [63] log likelihood: -20203.104319
EM: Round [64] log likelihood: -20203.085204
EM: Round [65] log likelihood: -20203.066236
EM: Round [66] log likelihood: -20203.047411
EM: Round [67] log likelihood: -20203.028728
EM: Round [68] log likelihood: -20203.010185
EM: Round [69] log likelihood: -20202.991781
EM: Round [70] log likelihood: -20202.973513
EM: Round [71] log likelihood: -20202.955379
EM: Round [72] log likelihood: -20202.937379
EM: Round [73] log likelihood: -20202.919510
EM: Round [74] log likelihood: -20202.901771
EM: Round [75] log likelihood: -20202.884160
EM: Round [76] log likelihood: -20202.866675
EM: Round [77] log likelihood: -20202.849315
EM: Round [78] log likelihood: -20202.832079
EM: Round [79] log likelihood: -20202.814964
EM: Round [80] log likelihood: -20202.797970
EM: Round [81] log likelihood: -20202.781094
EM: Round [82] log likelihood: -20202.764337
EM: Round [83] log likelihood: -20202.747695
EM: Round [84] log likelihood: -20202.731168
EM: Round [85] log likelihood: -20202.714754
EM: Round [86] log likelihood: -20202.698453
EM: Round [87] log likelihood: -20202.682262
EM: Round [88] log likelihood: -20202.666181
EM: Round [89] log likelihood: -20202.650207
EM: Round [90] log likelihood: -20202.634341
EM: Round [91] log likelihood: -20202.618581
EM: Round [92] log likelihood: -20202.602925
EM: Round [93] log likelihood: -20202.587372
EM: Round [94] log likelihood: -20202.571922
EM: Round [95] log likelihood: -20202.556573
EM: Round [96] log likelihood: -20202.541323
EM: Round [97] log likelihood: -20202.526173
EM: Round [98] log likelihood: -20202.511120
EM: Round [99] log likelihood: -20202.496165
EM: Round [100] log likelihood: -20202.481304
EM: Round [101] log likelihood: -20202.466539
EM: Round [102] log likelihood: -20202.451867
EM: Round [103] log likelihood: -20202.437288
EM: Round [104] log likelihood: -20202.422800
EM: Round [105] log likelihood: -20202.408403
EM: Round [106] log likelihood: -20202.394096
EM: Round [107] log likelihood: -20202.379878
EM: Round [108] log likelihood: -20202.365747
EM: Round [109] log likelihood: -20202.351704
EM: Round [110] log likelihood: -20202.337746
EM: Round [111] log likelihood: -20202.323874
EM: Round [112] log likelihood: -20202.310086
EM: Round [113] log likelihood: -20202.296382
EM: Round [114] log likelihood: -20202.282760
EM: Round [115] log likelihood: -20202.269220
EM: Round [116] log likelihood: -20202.255762
EM: Round [117] log likelihood: -20202.242383
EM: Round [118] log likelihood: -20202.229084
EM: Round [119] log likelihood: -20202.215863
EM: Round [120] log likelihood: -20202.202721
EM: Round [121] log likelihood: -20202.189655
EM: Round [122] log likelihood: -20202.176666
EM: Round [123] log likelihood: -20202.163753
EM: Round [124] log likelihood: -20202.150914
EM: Round [125] log likelihood: -20202.138150
EM: Round [126] log likelihood: -20202.125459
EM: Round [127] log likelihood: -20202.112841
EM: Round [128] log likelihood: -20202.100295
EM: Round [129] log likelihood: -20202.087820
EM: Round [130] log likelihood: -20202.075417
EM: Round [131] log likelihood: -20202.063083
EM: Round [132] log likelihood: -20202.050819
EM: Round [133] log likelihood: -20202.038624
EM: Round [134] log likelihood: -20202.026497
EM: Round [135] log likelihood: -20202.014438
EM: Round [136] log likelihood: -20202.002445
EM: Round [137] log likelihood: -20201.990519
EM: Round [138] log likelihood: -20201.978659
EM: Round [139] log likelihood: -20201.966864
EM: Round [140] log likelihood: -20201.955134
EM: Round [141] log likelihood: -20201.943468
EM: Round [142] log likelihood: -20201.931865
EM: Round [143] log likelihood: -20201.920325
EM: Round [144] log likelihood: -20201.908847
EM: Round [145] log likelihood: -20201.897431
EM: Round [146] log likelihood: -20201.886077
EM: Round [147] log likelihood: -20201.874783
EM: Round [148] log likelihood: -20201.863550
EM: Round [149] log likelihood: -20201.852376
EM: Round [150] log likelihood: -20201.841262
EM: Round [151] log likelihood: -20201.830206
EM: Round [152] log likelihood: -20201.819209
EM: Round [153] log likelihood: -20201.808269
EM: Round [154] log likelihood: -20201.797386
EM: Round [155] log likelihood: -20201.786561
EM: Round [156] log likelihood: -20201.775791
EM: Round [157] log likelihood: -20201.765078
EM: Round [158] log likelihood: -20201.754419
EM: Round [159] log likelihood: -20201.743816
EM: Round [160] log likelihood: -20201.733267
EM: Round [161] log likelihood: -20201.722772
EM: Round [162] log likelihood: -20201.712331
EM: Round [163] log likelihood: -20201.701943
EM: Round [164] log likelihood: -20201.691608
EM: Round [165] log likelihood: -20201.681325
EM: Round [166] log likelihood: -20201.671093
EM: Round [167] log likelihood: -20201.660914
EM: Round [168] log likelihood: -20201.650785
EM: Round [169] log likelihood: -20201.640707
EM: Round [170] log likelihood: -20201.630679
EM: Round [171] log likelihood: -20201.620701
EM: Round [172] log likelihood: -20201.610773
EM: Round [173] log likelihood: -20201.600894
EM: Round [174] log likelihood: -20201.591063
EM: Round [175] log likelihood: -20201.581281
EM: Round [176] log likelihood: -20201.571546
EM: Round [177] log likelihood: -20201.561860
EM: Round [178] log likelihood: -20201.552220
EM: Round [179] log likelihood: -20201.542628
EM: Round [180] log likelihood: -20201.533082
EM: Round [181] log likelihood: -20201.523582
EM: Round [182] log likelihood: -20201.514127
EM: Round [183] log likelihood: -20201.504719
EM: Round [184] log likelihood: -20201.495355
EM: Round [185] log likelihood: -20201.486037
EM: Round [186] log likelihood: -20201.476762
EM: Round [187] log likelihood: -20201.467532
EM: Round [188] log likelihood: -20201.458346
EM: Round [189] log likelihood: -20201.449203
EM: Round [190] log likelihood: -20201.440103
EM: Round [191] log likelihood: -20201.431047
EM: Round [192] log likelihood: -20201.422032
EM: Round [193] log likelihood: -20201.413060
EM: Round [194] log likelihood: -20201.404130
EM: Round [195] log likelihood: -20201.395242
EM: Round [196] log likelihood: -20201.386395
EM: Round [197] log likelihood: -20201.377589
EM: Round [198] log likelihood: -20201.368823
EM: Round [199] log likelihood: -20201.360098
EM: Round [200] log likelihood: -20201.351414
EM: Round [201] log likelihood: -20201.342769
EM: Round [202] log likelihood: -20201.334164
EM: Round [203] log likelihood: -20201.325598
EM: Round [204] log likelihood: -20201.317071
EM: Round [205] log likelihood: -20201.308583
EM: Round [206] log likelihood: -20201.300133
EM: Round [207] log likelihood: -20201.291722
EM: Round [208] log likelihood: -20201.283348
EM: Round [209] log likelihood: -20201.275013
EM: Round [210] log likelihood: -20201.266715
EM: Round [211] log likelihood: -20201.258454
EM: Round [212] log likelihood: -20201.250230
EM: Round [213] log likelihood: -20201.242042
EM: Round [214] log likelihood: -20201.233892
EM: Round [215] log likelihood: -20201.225777
EM: Round [216] log likelihood: -20201.217698
EM: Round [217] log likelihood: -20201.209655
EM: Round [218] log likelihood: -20201.201648
EM: Round [219] log likelihood: -20201.193676
EM: Round [220] log likelihood: -20201.185738
EM: Round [221] log likelihood: -20201.177836
EM: Round [222] log likelihood: -20201.169968
EM: Round [223] log likelihood: -20201.162135
EM: Round [224] log likelihood: -20201.154335
EM: Round [225] log likelihood: -20201.146570
EM: Round [226] log likelihood: -20201.138838
EM: Round [227] log likelihood: -20201.131139
EM: Round [228] log likelihood: -20201.123474
EM: Round [229] log likelihood: -20201.115842
EM: Round [230] log likelihood: -20201.108243
EM: Round [231] log likelihood: -20201.100676
EM: Round [232] log likelihood: -20201.093141
EM: Round [233] log likelihood: -20201.085639
EM: Round [234] log likelihood: -20201.078169
EM: Round [235] log likelihood: -20201.070730
EM: Round [236] log likelihood: -20201.063323
EM: Round [237] log likelihood: -20201.055948
EM: Round [238] log likelihood: -20201.048603
EM: Round [239] log likelihood: -20201.041290
EM: Round [240] log likelihood: -20201.034007
EM: Round [241] log likelihood: -20201.026755
EM: Round [242] log likelihood: -20201.019533
EM: Round [243] log likelihood: -20201.012342
EM: Round [244] log likelihood: -20201.005180
EM: Round [245] log likelihood: -20200.998048
EM: Round [246] log likelihood: -20200.990946
EM: Round [247] log likelihood: -20200.983874
EM: Round [248] log likelihood: -20200.976831
EM: Round [249] log likelihood: -20200.969816
EM: Round [250] log likelihood: -20200.962831
EM: Round [251] log likelihood: -20200.955875
EM: Round [252] log likelihood: -20200.948947
EM: Round [253] log likelihood: -20200.942047
EM: Round [254] log likelihood: -20200.935176
EM: Round [255] log likelihood: -20200.928333
EM: Round [256] log likelihood: -20200.921518
EM: Round [257] log likelihood: -20200.914730
EM: Round [258] log likelihood: -20200.907970
EM: Round [259] log likelihood: -20200.901238
EM: Round [260] log likelihood: -20200.894532
EM: Round [261] log likelihood: -20200.887854
EM: Round [262] log likelihood: -20200.881203
EM: Round [263] log likelihood: -20200.874579
EM: Round [264] log likelihood: -20200.867981
EM: Round [265] log likelihood: -20200.861409
EM: Round [266] log likelihood: -20200.854864
EM: Round [267] log likelihood: -20200.848345
EM: Round [268] log likelihood: -20200.841852
EM: Round [269] log likelihood: -20200.835385
EM: Round [270] log likelihood: -20200.828943
EM: Round [271] log likelihood: -20200.822527
EM: Round [272] log likelihood: -20200.816137
EM: Round [273] log likelihood: -20200.809772
EM: Round [274] log likelihood: -20200.803432
EM: Round [275] log likelihood: -20200.797116
EM: Round [276] log likelihood: -20200.790826
EM: Round [277] log likelihood: -20200.784560
EM: Round [278] log likelihood: -20200.778319
EM: Round [279] log likelihood: -20200.772103
EM: Round [280] log likelihood: -20200.765910
EM: Round [281] log likelihood: -20200.759742
EM: Round [282] log likelihood: -20200.753598
EM: Round [283] log likelihood: -20200.747477
EM: Round [284] log likelihood: -20200.741380
EM: Round [285] log likelihood: -20200.735307
EM: Round [286] log likelihood: -20200.729258
EM: Round [287] log likelihood: -20200.723231
EM: Round [288] log likelihood: -20200.717228
EM: Round [289] log likelihood: -20200.711248
EM: Round [290] log likelihood: -20200.705291
EM: Round [291] log likelihood: -20200.699357
EM: Round [292] log likelihood: -20200.693446
EM: Round [293] log likelihood: -20200.687557
EM: Round [294] log likelihood: -20200.681690
EM: Round [295] log likelihood: -20200.675846
EM: Round [296] log likelihood: -20200.670024
EM: Round [297] log likelihood: -20200.664224
EM: Round [298] log likelihood: -20200.658447
EM: Round [299] log likelihood: -20200.652691
EM: Round [300] log likelihood: -20200.646956
EM: Round [301] log likelihood: -20200.641244
EM: Round [302] log likelihood: -20200.635553
EM: Round [303] log likelihood: -20200.629883
EM: Round [304] log likelihood: -20200.624235
EM: Round [305] log likelihood: -20200.618607
EM: Round [306] log likelihood: -20200.613001
EM: Round [307] log likelihood: -20200.607416
EM: Round [308] log likelihood: -20200.601852
EM: Round [309] log likelihood: -20200.596308
EM: Round [310] log likelihood: -20200.590785
EM: Round [311] log likelihood: -20200.585282
EM: Round [312] log likelihood: -20200.579800
EM: Round [313] log likelihood: -20200.574338
EM: Round [314] log likelihood: -20200.568897
EM: Round [315] log likelihood: -20200.563475
EM: Round [316] log likelihood: -20200.558073
EM: Round [317] log likelihood: -20200.552692
EM: Round [318] log likelihood: -20200.547330
EM: Round [319] log likelihood: -20200.541988
EM: Round [320] log likelihood: -20200.536665
EM: Round [321] log likelihood: -20200.531362
EM: Round [322] log likelihood: -20200.526078
EM: Round [323] log likelihood: -20200.520813
EM: Round [324] log likelihood: -20200.515568
EM: Round [325] log likelihood: -20200.510342
EM: Round [326] log likelihood: -20200.505134
EM: Round [327] log likelihood: -20200.499946
EM: Round [328] log likelihood: -20200.494776
EM: Round [329] log likelihood: -20200.489625
EM: Round [330] log likelihood: -20200.484493
EM: Round [331] log likelihood: -20200.479379
EM: Round [332] log likelihood: -20200.474284
EM: Round [333] log likelihood: -20200.469207
EM: Round [334] log likelihood: -20200.464148
EM: Round [335] log likelihood: -20200.459107
EM: Round [336] log likelihood: -20200.454084
EM: Round [337] log likelihood: -20200.449080
EM: Round [338] log likelihood: -20200.444093
EM: Round [339] log likelihood: -20200.439124
EM: Round [340] log likelihood: -20200.434172
EM: Round [341] log likelihood: -20200.429239
EM: Round [342] log likelihood: -20200.424323
EM: Round [343] log likelihood: -20200.419424
EM: Round [344] log likelihood: -20200.414542
EM: Round [345] log likelihood: -20200.409678
EM: Round [346] log likelihood: -20200.404831
EM: Round [347] log likelihood: -20200.400001
EM: Round [348] log likelihood: -20200.395189
EM: Round [349] log likelihood: -20200.390393
EM: Round [350] log likelihood: -20200.385614
EM: Round [351] log likelihood: -20200.380852
EM: Round [352] log likelihood: -20200.376106
EM: Round [353] log likelihood: -20200.371377
EM: Round [354] log likelihood: -20200.366665
EM: Round [355] log likelihood: -20200.361969
EM: Round [356] log likelihood: -20200.357289
EM: Round [357] log likelihood: -20200.352626
EM: Round [358] log likelihood: -20200.347979
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EM: Round [360] log likelihood: -20200.338733
EM: Round [361] log likelihood: -20200.334134
EM: Round [362] log likelihood: -20200.329551
EM: Round [363] log likelihood: -20200.324984
EM: Round [364] log likelihood: -20200.320433
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EM: Round [366] log likelihood: -20200.311377
EM: Round [367] log likelihood: -20200.306873
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EM: Round [369] log likelihood: -20200.297910
EM: Round [370] log likelihood: -20200.293452
EM: Round [371] log likelihood: -20200.289009
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EM: Round [374] log likelihood: -20200.275771
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EM: Round [401] log likelihood: -20200.162482
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EM: Round [404] log likelihood: -20200.150513
EM: Round [405] log likelihood: -20200.146550
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EM: Round [410] log likelihood: -20200.126927
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EM: Round [412] log likelihood: -20200.119168
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EM: Round [421] log likelihood: -20200.084871
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EM: Round [433] log likelihood: -20200.040669
EM: Round [434] log likelihood: -20200.037062
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EM: Round [894] log likelihood: -20199.123303
EM: Round [895] log likelihood: -20199.122296
EM: Round [896] log likelihood: -20199.121291
EM: Round [897] log likelihood: -20199.120289
EM: Round [898] log likelihood: -20199.119289
EM: Round [899] log likelihood: -20199.118291
EM: Round [900] log likelihood: -20199.117296
EM: Round [901] log likelihood: -20199.116304
EM: Round [902] log likelihood: -20199.115314
EM: Round [903] log likelihood: -20199.114326
EM: Round [904] log likelihood: -20199.113341
EM: Round [905] log likelihood: -20199.112359
EM: Round [906] log likelihood: -20199.111379
EM: Round [907] log likelihood: -20199.110401
EM: Round [908] log likelihood: -20199.109426
EM: Round [909] log likelihood: -20199.108453
EM: Round [910] log likelihood: -20199.107483
EM: Round [911] log likelihood: -20199.106515
EM: Round [912] log likelihood: -20199.105549
EM: Round [913] log likelihood: -20199.104586
EM: Round [914] log likelihood: -20199.103625
EM: Round [915] log likelihood: -20199.102667
EM: Round [916] log likelihood: -20199.101711
EM: Round [917] log likelihood: -20199.100758
EM: Round [918] log likelihood: -20199.099806
EM: Round [919] log likelihood: -20199.098858
EM: Round [920] log likelihood: -20199.097911
EM: Round [921] log likelihood: -20199.096967
EM: Round [922] log likelihood: -20199.096025
EM: Round [923] log likelihood: -20199.095086
EM: Round [924] log likelihood: -20199.094149
EM: Round [925] log likelihood: -20199.093214
EM: Round [926] log likelihood: -20199.092282
EM: Round [927] log likelihood: -20199.091352
EM: Round [928] log likelihood: -20199.090424
EM: Round [929] log likelihood: -20199.089498
EM: Round [930] log likelihood: -20199.088575
EM: Round [931] log likelihood: -20199.087654
EM: Round [932] log likelihood: -20199.086736
EM: Round [933] log likelihood: -20199.085819
EM: Round [934] log likelihood: -20199.084905
EM: Round [935] log likelihood: -20199.083993
EM: Round [936] log likelihood: -20199.083084
EM: Round [937] log likelihood: -20199.082177
EM: Round [938] log likelihood: -20199.081272
EM: Round [939] log likelihood: -20199.080369
EM: Round [940] log likelihood: -20199.079468
EM: Round [941] log likelihood: -20199.078570
EM: Round [942] log likelihood: -20199.077674
EM: Round [943] log likelihood: -20199.076780
EM: Round [944] log likelihood: -20199.075888
EM: Round [945] log likelihood: -20199.074999
EM: Round [946] log likelihood: -20199.074112
EM: Round [947] log likelihood: -20199.073226
EM: Round [948] log likelihood: -20199.072344
EM: Round [949] log likelihood: -20199.071463
EM: Round [950] log likelihood: -20199.070584
EM: Round [951] log likelihood: -20199.069708
EM: Round [952] log likelihood: -20199.068834
EM: Round [953] log likelihood: -20199.067962
EM: Round [954] log likelihood: -20199.067092
EM: Round [955] log likelihood: -20199.066224
EM: Round [956] log likelihood: -20199.065359
EM: Round [957] log likelihood: -20199.064495
EM: Round [958] log likelihood: -20199.063634
EM: Round [959] log likelihood: -20199.062775
EM: Round [960] log likelihood: -20199.061918
EM: Round [961] log likelihood: -20199.061063
EM: Round [962] log likelihood: -20199.060210
EM: Round [963] log likelihood: -20199.059359
EM: Round [964] log likelihood: -20199.058510
EM: Round [965] log likelihood: -20199.057664
EM: Round [966] log likelihood: -20199.056819
EM: Round [967] log likelihood: -20199.055977
EM: Round [968] log likelihood: -20199.055136
EM: Round [969] log likelihood: -20199.054298
EM: Round [970] log likelihood: -20199.053462
EM: Round [971] log likelihood: -20199.052628
EM: Round [972] log likelihood: -20199.051796
EM: Round [973] log likelihood: -20199.050966
EM: Round [974] log likelihood: -20199.050138
EM: Round [975] log likelihood: -20199.049312
EM: Round [976] log likelihood: -20199.048488
EM: Round [977] log likelihood: -20199.047666
EM: Round [978] log likelihood: -20199.046846
EM: Round [979] log likelihood: -20199.046028
EM: Round [980] log likelihood: -20199.045212
EM: Round [981] log likelihood: -20199.044398
EM: Round [982] log likelihood: -20199.043586
EM: Round [983] log likelihood: -20199.042776
EM: Round [984] log likelihood: -20199.041968
EM: Round [985] log likelihood: -20199.041162
EM: Round [986] log likelihood: -20199.040358
EM: Round [987] log likelihood: -20199.039557
EM: Round [988] log likelihood: -20199.038756
EM: Round [989] log likelihood: -20199.037958
EM: Round [990] log likelihood: -20199.037162
EM: Round [991] log likelihood: -20199.036368
EM: Round [992] log likelihood: -20199.035576
EM: Round [993] log likelihood: -20199.034786
EM: Round [994] log likelihood: -20199.033997
EM: Round [995] log likelihood: -20199.033211
EM: Round [996] log likelihood: -20199.032426
EM: Round [997] log likelihood: -20199.031644
EM: Round [998] log likelihood: -20199.030863
EM: Round [999] log likelihood: -20199.030084
EM: Round [1000] log likelihood: -20199.029308
EM: Round [1001] log likelihood: -20199.028533
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz: 294568972
Execution Time = 5.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/fi_workdir/microH.dat
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.b9RdbAI3hE/fi_workdir/microH.dat /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/microH.dat /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.b9RdbAI3hE --json_outfile /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.b9RdbAI3hE --json_outfile /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1
Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --html_output /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --html_output /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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 [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000261235.1]
WARNING, no entry stored in dbm for [ENSG00000261235.1]
WARNING, no entry stored in dbm for [ENSG00000261235.1]
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 [ENSG00000237813.4]
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 [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 [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000254083.6]
WARNING, no entry stored in dbm for [ENSG00000254083.6]
WARNING, no entry stored in dbm for [ENSG00000254083.6]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory