Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/9e8ad4c9d09e3b72a867a0fd24f2b4/786-O_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/33368427b9e24a79ad3528c46ec03b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/33368427b9e24a79ad3528c46ec03b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/9e8ad4c9d09e3b72a867a0fd24f2b4/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/58227e1c14ac14aafed9910bff60a2/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/cytoBand.txt
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed
-parsing GTF file: /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.bed.tabix.ok
Running: samtools faidx /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.MY73Cq6J85/fi_workdir --reads "/tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:09:39 ..... started STAR run
Jun 08 10:09:39 ..... loading genome
Jun 08 10:11:25 ... generating Suffix Array index
Jun 08 10:15:17 ... completed Suffix Array index
Jun 08 10:15:18 ..... processing annotations GTF
Jun 08 10:15:18 ..... inserting junctions into the genome indices
Jun 08 10:16:19 ..... started mapping
Jun 08 11:23:19 ..... finished mapping
Jun 08 11:23:21 ..... started sorting BAM
Jun 08 11:23:22 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
* Running CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
Execution Time = 73.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.MY73Cq6J85/fi_workdir --reads "/tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
11:23:38 : INFO : Done.
Execution Time = 0.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
-parsing /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
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[2360000] -done parsing /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'exons hit < 2' => 13,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
'low complexity anchor region' => 26,
'num genes matched < 2' => 14,
'per_id < 96' => 13903,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 463,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
'seq-similar region overlap' => 28,
' ** passed ** ' => 47523,
'small anchor length' => 277,
'excessive soft clipping' => 15273
};
-writing fusion junction support info.
Execution Time = 1.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[159000] -fusion SPANNING read extraction for scaff: AC008969.1--SMARCA4
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[47000] -fusion SPANNING read extraction for scaff: BNC2--AL358117.1
[1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[70000] -fusion SPANNING read extraction for scaff: DHX38--AMPD1
[1000] -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L
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[38000] -fusion SPANNING read extraction for scaff: HMGB3P23--ACO1
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[15000] -fusion SPANNING read extraction for scaff: LHCGR--STON1
[1000] -fusion SPANNING read extraction for scaff: LHCGR--GTF2A1L
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[773000] -fusion SPANNING read extraction for scaff: LMNA--MEX3A
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[195000] -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1
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[34000] -fusion SPANNING read extraction for scaff: MTAP--AL157937.1
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[29000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[71000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[219000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[39000] -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1
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[14000] -fusion SPANNING read extraction for scaff: TAS2R14--PRH2
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[36000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[39000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[23000] -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 16635,
'lacks exon overlap' => 30926
};
Execution Time = 3.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -9094.063994
EM: Round [1] log likelihood: -9092.960778
EM: Round [2] log likelihood: -9092.956805
EM: Round [3] log likelihood: -9092.953158
EM: Round [4] log likelihood: -9092.949527
EM: Round [5] log likelihood: -9092.945910
EM: Round [6] log likelihood: -9092.942308
EM: Round [7] log likelihood: -9092.938721
EM: Round [8] log likelihood: -9092.935147
EM: Round [9] log likelihood: -9092.931588
EM: Round [10] log likelihood: -9092.928043
EM: Round [11] log likelihood: -9092.924512
EM: Round [12] log likelihood: -9092.920995
EM: Round [13] log likelihood: -9092.917491
EM: Round [14] log likelihood: -9092.914001
EM: Round [15] log likelihood: -9092.910525
EM: Round [16] log likelihood: -9092.907062
EM: Round [17] log likelihood: -9092.903613
EM: Round [18] log likelihood: -9092.900177
EM: Round [19] log likelihood: -9092.896754
EM: Round [20] log likelihood: -9092.893344
EM: Round [21] log likelihood: -9092.889947
EM: Round [22] log likelihood: -9092.886563
EM: Round [23] log likelihood: -9092.883191
EM: Round [24] log likelihood: -9092.879833
EM: Round [25] log likelihood: -9092.876487
EM: Round [26] log likelihood: -9092.873153
EM: Round [27] log likelihood: -9092.869832
EM: Round [28] log likelihood: -9092.866524
EM: Round [29] log likelihood: -9092.863227
EM: Round [30] log likelihood: -9092.859943
EM: Round [31] log likelihood: -9092.856671
EM: Round [32] log likelihood: -9092.853411
EM: Round [33] log likelihood: -9092.850163
EM: Round [34] log likelihood: -9092.846927
EM: Round [35] log likelihood: -9092.843702
EM: Round [36] log likelihood: -9092.840489
EM: Round [37] log likelihood: -9092.837288
EM: Round [38] log likelihood: -9092.834098
EM: Round [39] log likelihood: -9092.830920
EM: Round [40] log likelihood: -9092.827753
EM: Round [41] log likelihood: -9092.824597
EM: Round [42] log likelihood: -9092.821453
EM: Round [43] log likelihood: -9092.818320
EM: Round [44] log likelihood: -9092.815197
EM: Round [45] log likelihood: -9092.812086
EM: Round [46] log likelihood: -9092.808986
EM: Round [47] log likelihood: -9092.805897
EM: Round [48] log likelihood: -9092.802818
EM: Round [49] log likelihood: -9092.799750
EM: Round [50] log likelihood: -9092.796693
EM: Round [51] log likelihood: -9092.793646
EM: Round [52] log likelihood: -9092.790610
EM: Round [53] log likelihood: -9092.787584
EM: Round [54] log likelihood: -9092.784568
EM: Round [55] log likelihood: -9092.781563
EM: Round [56] log likelihood: -9092.778568
EM: Round [57] log likelihood: -9092.775584
EM: Round [58] log likelihood: -9092.772609
EM: Round [59] log likelihood: -9092.769644
EM: Round [60] log likelihood: -9092.766690
EM: Round [61] log likelihood: -9092.763745
EM: Round [62] log likelihood: -9092.760810
EM: Round [63] log likelihood: -9092.757885
EM: Round [64] log likelihood: -9092.754970
EM: Round [65] log likelihood: -9092.752064
EM: Round [66] log likelihood: -9092.749168
EM: Round [67] log likelihood: -9092.746281
EM: Round [68] log likelihood: -9092.743404
EM: Round [69] log likelihood: -9092.740537
EM: Round [70] log likelihood: -9092.737678
EM: Round [71] log likelihood: -9092.734830
EM: Round [72] log likelihood: -9092.731990
EM: Round [73] log likelihood: -9092.729159
EM: Round [74] log likelihood: -9092.726338
EM: Round [75] log likelihood: -9092.723526
EM: Round [76] log likelihood: -9092.720723
EM: Round [77] log likelihood: -9092.717929
EM: Round [78] log likelihood: -9092.715143
EM: Round [79] log likelihood: -9092.712367
EM: Round [80] log likelihood: -9092.709599
EM: Round [81] log likelihood: -9092.706840
EM: Round [82] log likelihood: -9092.704090
EM: Round [83] log likelihood: -9092.701349
EM: Round [84] log likelihood: -9092.698616
EM: Round [85] log likelihood: -9092.695892
EM: Round [86] log likelihood: -9092.693176
EM: Round [87] log likelihood: -9092.690469
EM: Round [88] log likelihood: -9092.687770
EM: Round [89] log likelihood: -9092.685080
EM: Round [90] log likelihood: -9092.682398
EM: Round [91] log likelihood: -9092.679724
EM: Round [92] log likelihood: -9092.677058
EM: Round [93] log likelihood: -9092.674401
EM: Round [94] log likelihood: -9092.671751
EM: Round [95] log likelihood: -9092.669110
EM: Round [96] log likelihood: -9092.666477
EM: Round [97] log likelihood: -9092.663852
EM: Round [98] log likelihood: -9092.661234
EM: Round [99] log likelihood: -9092.658625
EM: Round [100] log likelihood: -9092.656023
EM: Round [101] log likelihood: -9092.653430
EM: Round [102] log likelihood: -9092.650844
EM: Round [103] log likelihood: -9092.648266
EM: Round [104] log likelihood: -9092.645695
EM: Round [105] log likelihood: -9092.643132
EM: Round [106] log likelihood: -9092.640577
EM: Round [107] log likelihood: -9092.638029
EM: Round [108] log likelihood: -9092.635489
EM: Round [109] log likelihood: -9092.632956
EM: Round [110] log likelihood: -9092.630431
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Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam"
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || :
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords
CMD: touch /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3 --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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir
-done, see /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -8526.691053
EM: Round [1] log likelihood: -8526.483673
EM: Round [2] log likelihood: -8526.480720
EM: Round [3] log likelihood: -8526.477876
EM: Round [4] log likelihood: -8526.475042
EM: Round [5] log likelihood: -8526.472217
EM: Round [6] log likelihood: -8526.469400
EM: Round [7] log likelihood: -8526.466593
EM: Round [8] log likelihood: -8526.463795
EM: Round [9] log likelihood: -8526.461006
EM: Round [10] log likelihood: -8526.458225
EM: Round [11] log likelihood: -8526.455454
EM: Round [12] log likelihood: -8526.452691
EM: Round [13] log likelihood: -8526.449937
EM: Round [14] log likelihood: -8526.447192
EM: Round [15] log likelihood: -8526.444455
EM: Round [16] log likelihood: -8526.441727
EM: Round [17] log likelihood: -8526.439008
EM: Round [18] log likelihood: -8526.436297
EM: Round [19] log likelihood: -8526.433594
EM: Round [20] log likelihood: -8526.430900
EM: Round [21] log likelihood: -8526.428214
EM: Round [22] log likelihood: -8526.425537
EM: Round [23] log likelihood: -8526.422867
EM: Round [24] log likelihood: -8526.420206
EM: Round [25] log likelihood: -8526.417553
EM: Round [26] log likelihood: -8526.414908
EM: Round [27] log likelihood: -8526.412272
EM: Round [28] log likelihood: -8526.409643
EM: Round [29] log likelihood: -8526.407022
EM: Round [30] log likelihood: -8526.404409
EM: Round [31] log likelihood: -8526.401804
EM: Round [32] log likelihood: -8526.399207
EM: Round [33] log likelihood: -8526.396618
EM: Round [34] log likelihood: -8526.394036
EM: Round [35] log likelihood: -8526.391462
EM: Round [36] log likelihood: -8526.388896
EM: Round [37] log likelihood: -8526.386337
EM: Round [38] log likelihood: -8526.383786
EM: Round [39] log likelihood: -8526.381243
EM: Round [40] log likelihood: -8526.378706
EM: Round [41] log likelihood: -8526.376178
EM: Round [42] log likelihood: -8526.373657
EM: Round [43] log likelihood: -8526.371143
EM: Round [44] log likelihood: -8526.368636
EM: Round [45] log likelihood: -8526.366137
EM: Round [46] log likelihood: -8526.363645
EM: Round [47] log likelihood: -8526.361161
EM: Round [48] log likelihood: -8526.358683
EM: Round [49] log likelihood: -8526.356213
EM: Round [50] log likelihood: -8526.353749
EM: Round [51] log likelihood: -8526.351293
EM: Round [52] log likelihood: -8526.348844
EM: Round [53] log likelihood: -8526.346402
EM: Round [54] log likelihood: -8526.343966
EM: Round [55] log likelihood: -8526.341538
EM: Round [56] log likelihood: -8526.339117
EM: Round [57] log likelihood: -8526.336702
EM: Round [58] log likelihood: -8526.334294
EM: Round [59] log likelihood: -8526.331893
EM: Round [60] log likelihood: -8526.329499
EM: Round [61] log likelihood: -8526.327111
EM: Round [62] log likelihood: -8526.324730
EM: Round [63] log likelihood: -8526.322356
EM: Round [64] log likelihood: -8526.319988
EM: Round [65] log likelihood: -8526.317627
EM: Round [66] log likelihood: -8526.315272
EM: Round [67] log likelihood: -8526.312924
EM: Round [68] log likelihood: -8526.310582
EM: Round [69] log likelihood: -8526.308247
EM: Round [70] log likelihood: -8526.305918
EM: Round [71] log likelihood: -8526.303596
EM: Round [72] log likelihood: -8526.301279
EM: Round [73] log likelihood: -8526.298970
EM: Round [74] log likelihood: -8526.296666
EM: Round [75] log likelihood: -8526.294369
EM: Round [76] log likelihood: -8526.292077
EM: Round [77] log likelihood: -8526.289792
EM: Round [78] log likelihood: -8526.287514
EM: Round [79] log likelihood: -8526.285241
EM: Round [80] log likelihood: -8526.282974
EM: Round [81] log likelihood: -8526.280714
EM: Round [82] log likelihood: -8526.278459
EM: Round [83] log likelihood: -8526.276211
EM: Round [84] log likelihood: -8526.273968
EM: Round [85] log likelihood: -8526.271731
EM: Round [86] log likelihood: -8526.269501
EM: Round [87] log likelihood: -8526.267276
EM: Round [88] log likelihood: -8526.265057
EM: Round [89] log likelihood: -8526.262843
EM: Round [90] log likelihood: -8526.260636
EM: Round [91] log likelihood: -8526.258434
EM: Round [92] log likelihood: -8526.256238
EM: Round [93] log likelihood: -8526.254048
EM: Round [94] log likelihood: -8526.251864
EM: Round [95] log likelihood: -8526.249685
EM: Round [96] log likelihood: -8526.247512
EM: Round [97] log likelihood: -8526.245344
EM: Round [98] log likelihood: -8526.243182
EM: Round [99] log likelihood: -8526.241025
EM: Round [100] log likelihood: -8526.238874
EM: Round [101] log likelihood: -8526.236729
EM: Round [102] log likelihood: -8526.234589
EM: Round [103] log likelihood: -8526.232454
EM: Round [104] log likelihood: -8526.230325
EM: Round [105] log likelihood: -8526.228202
EM: Round [106] log likelihood: -8526.226083
EM: Round [107] log likelihood: -8526.223970
EM: Round [108] log likelihood: -8526.221862
EM: Round [109] log likelihood: -8526.219760
EM: Round [110] log likelihood: -8526.217663
EM: Round [111] log likelihood: -8526.215571
EM: Round [112] log likelihood: -8526.213484
EM: Round [113] log likelihood: -8526.211403
EM: Round [114] log likelihood: -8526.209326
EM: Round [115] log likelihood: -8526.207255
EM: Round [116] log likelihood: -8526.205189
EM: Round [117] log likelihood: -8526.203128
EM: Round [118] log likelihood: -8526.201073
EM: Round [119] log likelihood: -8526.199022
EM: Round [120] log likelihood: -8526.196976
EM: Round [121] log likelihood: -8526.194935
EM: Round [122] log likelihood: -8526.192900
EM: Round [123] log likelihood: -8526.190869
EM: Round [124] log likelihood: -8526.188843
EM: Round [125] log likelihood: -8526.186822
EM: Round [126] log likelihood: -8526.184806
EM: Round [127] log likelihood: -8526.182795
EM: Round [128] log likelihood: -8526.180789
EM: Round [129] log likelihood: -8526.178788
EM: Round [130] log likelihood: -8526.176791
EM: Round [131] log likelihood: -8526.174799
EM: Round [132] log likelihood: -8526.172812
EM: Round [133] log likelihood: -8526.170830
EM: Round [134] log likelihood: -8526.168852
EM: Round [135] log likelihood: -8526.166880
EM: Round [136] log likelihood: -8526.164911
EM: Round [137] log likelihood: -8526.162948
EM: Round [138] log likelihood: -8526.160989
EM: Round [139] log likelihood: -8526.159035
EM: Round [140] log likelihood: -8526.157086
EM: Round [141] log likelihood: -8526.155141
EM: Round [142] log likelihood: -8526.153200
EM: Round [143] log likelihood: -8526.151264
EM: Round [144] log likelihood: -8526.149333
EM: Round [145] log likelihood: -8526.147406
EM: Round [146] log likelihood: -8526.145484
EM: Round [147] log likelihood: -8526.143566
EM: Round [148] log likelihood: -8526.141653
EM: Round [149] log likelihood: -8526.139744
EM: Round [150] log likelihood: -8526.137839
EM: Round [151] log likelihood: -8526.135939
EM: Round [152] log likelihood: -8526.134044
EM: Round [153] log likelihood: -8526.132152
EM: Round [154] log likelihood: -8526.130265
EM: Round [155] log likelihood: -8526.128383
EM: Round [156] log likelihood: -8526.126504
EM: Round [157] log likelihood: -8526.124630
EM: Round [158] log likelihood: -8526.122760
EM: Round [159] log likelihood: -8526.120895
EM: Round [160] log likelihood: -8526.119033
EM: Round [161] log likelihood: -8526.117176
EM: Round [162] log likelihood: -8526.115323
EM: Round [163] log likelihood: -8526.113475
EM: Round [164] log likelihood: -8526.111630
EM: Round [165] log likelihood: -8526.109790
EM: Round [166] log likelihood: -8526.107954
EM: Round [167] log likelihood: -8526.106121
EM: Round [168] log likelihood: -8526.104293
EM: Round [169] log likelihood: -8526.102470
EM: Round [170] log likelihood: -8526.100650
EM: Round [171] log likelihood: -8526.098834
EM: Round [172] log likelihood: -8526.097022
EM: Round [173] log likelihood: -8526.095214
EM: Round [174] log likelihood: -8526.093411
EM: Round [175] log likelihood: -8526.091611
EM: Round [176] log likelihood: -8526.089815
EM: Round [177] log likelihood: -8526.088023
EM: Round [178] log likelihood: -8526.086235
EM: Round [179] log likelihood: -8526.084451
EM: Round [180] log likelihood: -8526.082671
EM: Round [181] log likelihood: -8526.080895
EM: Round [182] log likelihood: -8526.079123
EM: Round [183] log likelihood: -8526.077354
EM: Round [184] log likelihood: -8526.075590
EM: Round [185] log likelihood: -8526.073829
EM: Round [186] log likelihood: -8526.072072
EM: Round [187] log likelihood: -8526.070319
EM: Round [188] log likelihood: -8526.068569
EM: Round [189] log likelihood: -8526.066824
EM: Round [190] log likelihood: -8526.065082
EM: Round [191] log likelihood: -8526.063344
EM: Round [192] log likelihood: -8526.061609
EM: Round [193] log likelihood: -8526.059879
EM: Round [194] log likelihood: -8526.058152
EM: Round [195] log likelihood: -8526.056428
EM: Round [196] log likelihood: -8526.054709
EM: Round [197] log likelihood: -8526.052993
EM: Round [198] log likelihood: -8526.051281
EM: Round [199] log likelihood: -8526.049572
EM: Round [200] log likelihood: -8526.047867
EM: Round [201] log likelihood: -8526.046165
EM: Round [202] log likelihood: -8526.044468
EM: Round [203] log likelihood: -8526.042773
EM: Round [204] log likelihood: -8526.041083
EM: Round [205] log likelihood: -8526.039395
EM: Round [206] log likelihood: -8526.037712
EM: Round [207] log likelihood: -8526.036032
EM: Round [208] log likelihood: -8526.034355
EM: Round [209] log likelihood: -8526.032682
EM: Round [210] log likelihood: -8526.031012
EM: Round [211] log likelihood: -8526.029346
EM: Round [212] log likelihood: -8526.027683
EM: Round [213] log likelihood: -8526.026024
EM: Round [214] log likelihood: -8526.024368
EM: Round [215] log likelihood: -8526.022716
EM: Round [216] log likelihood: -8526.021067
EM: Round [217] log likelihood: -8526.019421
EM: Round [218] log likelihood: -8526.017779
EM: Round [219] log likelihood: -8526.016140
EM: Round [220] log likelihood: -8526.014504
EM: Round [221] log likelihood: -8526.012872
EM: Round [222] log likelihood: -8526.011243
EM: Round [223] log likelihood: -8526.009617
EM: Round [224] log likelihood: -8526.007995
EM: Round [225] log likelihood: -8526.006376
EM: Round [226] log likelihood: -8526.004761
EM: Round [227] log likelihood: -8526.003148
EM: Round [228] log likelihood: -8526.001539
EM: Round [229] log likelihood: -8525.999933
EM: Round [230] log likelihood: -8525.998330
EM: Round [231] log likelihood: -8525.996731
EM: Round [232] log likelihood: -8525.995135
EM: Round [233] log likelihood: -8525.993542
EM: Round [234] log likelihood: -8525.991952
EM: Round [235] log likelihood: -8525.990365
EM: Round [236] log likelihood: -8525.988781
EM: Round [237] log likelihood: -8525.987201
EM: Round [238] log likelihood: -8525.985624
EM: Round [239] log likelihood: -8525.984050
EM: Round [240] log likelihood: -8525.982479
EM: Round [241] log likelihood: -8525.980911
EM: Round [242] log likelihood: -8525.979346
EM: Round [243] log likelihood: -8525.977784
EM: Round [244] log likelihood: -8525.976226
EM: Round [245] log likelihood: -8525.974670
EM: Round [246] log likelihood: -8525.973118
EM: Round [247] log likelihood: -8525.971568
EM: Round [248] log likelihood: -8525.970022
EM: Round [249] log likelihood: -8525.968478
EM: Round [250] log likelihood: -8525.966938
EM: Round [251] log likelihood: -8525.965401
EM: Round [252] log likelihood: -8525.963866
EM: Round [253] log likelihood: -8525.962335
EM: Round [254] log likelihood: -8525.960806
EM: Round [255] log likelihood: -8525.959281
EM: Round [256] log likelihood: -8525.957758
EM: Round [257] log likelihood: -8525.956239
EM: Round [258] log likelihood: -8525.954722
EM: Round [259] log likelihood: -8525.953208
EM: Round [260] log likelihood: -8525.951697
EM: Round [261] log likelihood: -8525.950189
EM: Round [262] log likelihood: -8525.948684
EM: Round [263] log likelihood: -8525.947182
EM: Round [264] log likelihood: -8525.945683
EM: Round [265] log likelihood: -8525.944186
EM: Round [266] log likelihood: -8525.942693
EM: Round [267] log likelihood: -8525.941202
EM: Round [268] log likelihood: -8525.939714
EM: Round [269] log likelihood: -8525.938229
EM: Round [270] log likelihood: -8525.936746
EM: Round [271] log likelihood: -8525.935267
EM: Round [272] log likelihood: -8525.933790
EM: Round [273] log likelihood: -8525.932316
EM: Round [274] log likelihood: -8525.930845
EM: Round [275] log likelihood: -8525.929377
EM: Round [276] log likelihood: -8525.927911
EM: Round [277] log likelihood: -8525.926448
EM: Round [278] log likelihood: -8525.924988
EM: Round [279] log likelihood: -8525.923531
EM: Round [280] log likelihood: -8525.922076
EM: Round [281] log likelihood: -8525.920624
EM: Round [282] log likelihood: -8525.919175
EM: Round [283] log likelihood: -8525.917728
EM: Round [284] log likelihood: -8525.916284
EM: Round [285] log likelihood: -8525.914843
EM: Round [286] log likelihood: -8525.913404
EM: Round [287] log likelihood: -8525.911968
EM: Round [288] log likelihood: -8525.910535
EM: Round [289] log likelihood: -8525.909104
EM: Round [290] log likelihood: -8525.907676
EM: Round [291] log likelihood: -8525.906251
EM: Round [292] log likelihood: -8525.904828
EM: Round [293] log likelihood: -8525.903408
EM: Round [294] log likelihood: -8525.901990
EM: Round [295] log likelihood: -8525.900575
EM: Round [296] log likelihood: -8525.899163
EM: Round [297] log likelihood: -8525.897753
EM: Round [298] log likelihood: -8525.896346
EM: Round [299] log likelihood: -8525.894941
EM: Round [300] log likelihood: -8525.893539
EM: Round [301] log likelihood: -8525.892139
EM: Round [302] log likelihood: -8525.890742
EM: Round [303] log likelihood: -8525.889348
EM: Round [304] log likelihood: -8525.887956
EM: Round [305] log likelihood: -8525.886566
EM: Round [306] log likelihood: -8525.885179
EM: Round [307] log likelihood: -8525.883794
EM: Round [308] log likelihood: -8525.882412
EM: Round [309] log likelihood: -8525.881033
EM: Round [310] log likelihood: -8525.879655
EM: Round [311] log likelihood: -8525.878281
EM: Round [312] log likelihood: -8525.876908
EM: Round [313] log likelihood: -8525.875539
EM: Round [314] log likelihood: -8525.874171
EM: Round [315] log likelihood: -8525.872806
EM: Round [316] log likelihood: -8525.871444
EM: Round [317] log likelihood: -8525.870084
EM: Round [318] log likelihood: -8525.868726
EM: Round [319] log likelihood: -8525.867371
EM: Round [320] log likelihood: -8525.866018
EM: Round [321] log likelihood: -8525.864667
EM: Round [322] log likelihood: -8525.863319
EM: Round [323] log likelihood: -8525.861973
EM: Round [324] log likelihood: -8525.860630
EM: Round [325] log likelihood: -8525.859289
EM: Round [326] log likelihood: -8525.857950
EM: Round [327] log likelihood: -8525.856614
EM: Round [328] log likelihood: -8525.855280
EM: Round [329] log likelihood: -8525.853948
EM: Round [330] log likelihood: -8525.852618
EM: Round [331] log likelihood: -8525.851291
EM: Round [332] log likelihood: -8525.849967
EM: Round [333] log likelihood: -8525.848644
EM: Round [334] log likelihood: -8525.847324
EM: Round [335] log likelihood: -8525.846006
EM: Round [336] log likelihood: -8525.844690
EM: Round [337] log likelihood: -8525.843377
EM: Round [338] log likelihood: -8525.842066
EM: Round [339] log likelihood: -8525.840757
EM: Round [340] log likelihood: -8525.839450
EM: Round [341] log likelihood: -8525.838146
EM: Round [342] log likelihood: -8525.836844
EM: Round [343] log likelihood: -8525.835544
EM: Round [344] log likelihood: -8525.834246
EM: Round [345] log likelihood: -8525.832950
EM: Round [346] log likelihood: -8525.831657
EM: Round [347] log likelihood: -8525.830366
EM: Round [348] log likelihood: -8525.829077
EM: Round [349] log likelihood: -8525.827791
EM: Round [350] log likelihood: -8525.826506
EM: Round [351] log likelihood: -8525.825224
EM: Round [352] log likelihood: -8525.823943
EM: Round [353] log likelihood: -8525.822665
EM: Round [354] log likelihood: -8525.821390
EM: Round [355] log likelihood: -8525.820116
EM: Round [356] log likelihood: -8525.818844
EM: Round [357] log likelihood: -8525.817575
EM: Round [358] log likelihood: -8525.816308
EM: Round [359] log likelihood: -8525.815042
EM: Round [360] log likelihood: -8525.813779
EM: Round [361] log likelihood: -8525.812518
EM: Round [362] log likelihood: -8525.811259
EM: Round [363] log likelihood: -8525.810003
EM: Round [364] log likelihood: -8525.808748
EM: Round [365] log likelihood: -8525.807495
EM: Round [366] log likelihood: -8525.806245
EM: Round [367] log likelihood: -8525.804997
EM: Round [368] log likelihood: -8525.803750
EM: Round [369] log likelihood: -8525.802506
EM: Round [370] log likelihood: -8525.801264
EM: Round [371] log likelihood: -8525.800024
EM: Round [372] log likelihood: -8525.798785
EM: Round [373] log likelihood: -8525.797549
EM: Round [374] log likelihood: -8525.796315
EM: Round [375] log likelihood: -8525.795083
EM: Round [376] log likelihood: -8525.793853
EM: Round [377] log likelihood: -8525.792625
EM: Round [378] log likelihood: -8525.791399
EM: Round [379] log likelihood: -8525.790175
EM: Round [380] log likelihood: -8525.788953
EM: Round [381] log likelihood: -8525.787733
EM: Round [382] log likelihood: -8525.786515
EM: Round [383] log likelihood: -8525.785299
EM: Round [384] log likelihood: -8525.784085
EM: Round [385] log likelihood: -8525.782873
EM: Round [386] log likelihood: -8525.781663
EM: Round [387] log likelihood: -8525.780455
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EM: Round [848] log likelihood: -8525.370351
EM: Round [849] log likelihood: -8525.369689
EM: Round [850] log likelihood: -8525.369027
EM: Round [851] log likelihood: -8525.368366
EM: Round [852] log likelihood: -8525.367706
EM: Round [853] log likelihood: -8525.367046
EM: Round [854] log likelihood: -8525.366387
EM: Round [855] log likelihood: -8525.365729
EM: Round [856] log likelihood: -8525.365071
EM: Round [857] log likelihood: -8525.364415
EM: Round [858] log likelihood: -8525.363759
EM: Round [859] log likelihood: -8525.363103
EM: Round [860] log likelihood: -8525.362448
EM: Round [861] log likelihood: -8525.361794
EM: Round [862] log likelihood: -8525.361141
EM: Round [863] log likelihood: -8525.360488
EM: Round [864] log likelihood: -8525.359837
EM: Round [865] log likelihood: -8525.359185
EM: Round [866] log likelihood: -8525.358535
EM: Round [867] log likelihood: -8525.357885
EM: Round [868] log likelihood: -8525.357236
EM: Round [869] log likelihood: -8525.356587
EM: Round [870] log likelihood: -8525.355939
EM: Round [871] log likelihood: -8525.355292
EM: Round [872] log likelihood: -8525.354646
EM: Round [873] log likelihood: -8525.354000
EM: Round [874] log likelihood: -8525.353355
EM: Round [875] log likelihood: -8525.352711
EM: Round [876] log likelihood: -8525.352067
EM: Round [877] log likelihood: -8525.351424
EM: Round [878] log likelihood: -8525.350782
EM: Round [879] log likelihood: -8525.350140
EM: Round [880] log likelihood: -8525.349499
EM: Round [881] log likelihood: -8525.348859
EM: Round [882] log likelihood: -8525.348219
EM: Round [883] log likelihood: -8525.347580
EM: Round [884] log likelihood: -8525.346942
EM: Round [885] log likelihood: -8525.346304
EM: Round [886] log likelihood: -8525.345667
EM: Round [887] log likelihood: -8525.345031
EM: Round [888] log likelihood: -8525.344395
EM: Round [889] log likelihood: -8525.343760
EM: Round [890] log likelihood: -8525.343126
EM: Round [891] log likelihood: -8525.342492
EM: Round [892] log likelihood: -8525.341859
EM: Round [893] log likelihood: -8525.341227
EM: Round [894] log likelihood: -8525.340595
EM: Round [895] log likelihood: -8525.339964
EM: Round [896] log likelihood: -8525.339334
EM: Round [897] log likelihood: -8525.338704
EM: Round [898] log likelihood: -8525.338075
EM: Round [899] log likelihood: -8525.337447
EM: Round [900] log likelihood: -8525.336819
EM: Round [901] log likelihood: -8525.336192
EM: Round [902] log likelihood: -8525.335566
EM: Round [903] log likelihood: -8525.334940
EM: Round [904] log likelihood: -8525.334315
EM: Round [905] log likelihood: -8525.333690
EM: Round [906] log likelihood: -8525.333066
EM: Round [907] log likelihood: -8525.332443
EM: Round [908] log likelihood: -8525.331821
EM: Round [909] log likelihood: -8525.331199
EM: Round [910] log likelihood: -8525.330577
EM: Round [911] log likelihood: -8525.329957
EM: Round [912] log likelihood: -8525.329337
EM: Round [913] log likelihood: -8525.328717
EM: Round [914] log likelihood: -8525.328099
EM: Round [915] log likelihood: -8525.327481
EM: Round [916] log likelihood: -8525.326863
EM: Round [917] log likelihood: -8525.326246
EM: Round [918] log likelihood: -8525.325630
EM: Round [919] log likelihood: -8525.325015
EM: Round [920] log likelihood: -8525.324400
EM: Round [921] log likelihood: -8525.323785
EM: Round [922] log likelihood: -8525.323172
EM: Round [923] log likelihood: -8525.322559
EM: Round [924] log likelihood: -8525.321946
EM: Round [925] log likelihood: -8525.321335
EM: Round [926] log likelihood: -8525.320723
EM: Round [927] log likelihood: -8525.320113
EM: Round [928] log likelihood: -8525.319503
EM: Round [929] log likelihood: -8525.318894
EM: Round [930] log likelihood: -8525.318285
EM: Round [931] log likelihood: -8525.317677
EM: Round [932] log likelihood: -8525.317070
EM: Round [933] log likelihood: -8525.316463
EM: Round [934] log likelihood: -8525.315857
EM: Round [935] log likelihood: -8525.315251
EM: Round [936] log likelihood: -8525.314646
EM: Round [937] log likelihood: -8525.314042
EM: Round [938] log likelihood: -8525.313438
EM: Round [939] log likelihood: -8525.312835
EM: Round [940] log likelihood: -8525.312233
EM: Round [941] log likelihood: -8525.311631
EM: Round [942] log likelihood: -8525.311029
EM: Round [943] log likelihood: -8525.310429
EM: Round [944] log likelihood: -8525.309829
EM: Round [945] log likelihood: -8525.309229
EM: Round [946] log likelihood: -8525.308630
EM: Round [947] log likelihood: -8525.308032
EM: Round [948] log likelihood: -8525.307434
EM: Round [949] log likelihood: -8525.306837
EM: Round [950] log likelihood: -8525.306241
EM: Round [951] log likelihood: -8525.305645
EM: Round [952] log likelihood: -8525.305050
EM: Round [953] log likelihood: -8525.304455
EM: Round [954] log likelihood: -8525.303861
EM: Round [955] log likelihood: -8525.303268
EM: Round [956] log likelihood: -8525.302675
EM: Round [957] log likelihood: -8525.302083
EM: Round [958] log likelihood: -8525.301491
EM: Round [959] log likelihood: -8525.300900
EM: Round [960] log likelihood: -8525.300309
EM: Round [961] log likelihood: -8525.299720
EM: Round [962] log likelihood: -8525.299130
EM: Round [963] log likelihood: -8525.298542
EM: Round [964] log likelihood: -8525.297953
EM: Round [965] log likelihood: -8525.297366
EM: Round [966] log likelihood: -8525.296779
EM: Round [967] log likelihood: -8525.296193
EM: Round [968] log likelihood: -8525.295607
EM: Round [969] log likelihood: -8525.295022
EM: Round [970] log likelihood: -8525.294437
EM: Round [971] log likelihood: -8525.293853
EM: Round [972] log likelihood: -8525.293270
EM: Round [973] log likelihood: -8525.292687
EM: Round [974] log likelihood: -8525.292104
EM: Round [975] log likelihood: -8525.291523
EM: Round [976] log likelihood: -8525.290942
EM: Round [977] log likelihood: -8525.290361
EM: Round [978] log likelihood: -8525.289781
EM: Round [979] log likelihood: -8525.289202
EM: Round [980] log likelihood: -8525.288623
EM: Round [981] log likelihood: -8525.288044
EM: Round [982] log likelihood: -8525.287467
EM: Round [983] log likelihood: -8525.286890
EM: Round [984] log likelihood: -8525.286313
EM: Round [985] log likelihood: -8525.285737
EM: Round [986] log likelihood: -8525.285162
EM: Round [987] log likelihood: -8525.284587
EM: Round [988] log likelihood: -8525.284013
EM: Round [989] log likelihood: -8525.283439
EM: Round [990] log likelihood: -8525.282866
EM: Round [991] log likelihood: -8525.282293
EM: Round [992] log likelihood: -8525.281721
EM: Round [993] log likelihood: -8525.281150
EM: Round [994] log likelihood: -8525.280579
EM: Round [995] log likelihood: -8525.280008
EM: Round [996] log likelihood: -8525.279439
EM: Round [997] log likelihood: -8525.278869
EM: Round [998] log likelihood: -8525.278301
EM: Round [999] log likelihood: -8525.277733
EM: Round [1000] log likelihood: -8525.277165
EM: Round [1001] log likelihood: -8525.276598
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 294645782
Execution Time = 5.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.MY73Cq6J85/fi_workdir/microH.dat
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.MY73Cq6J85/fi_workdir/microH.dat /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.MY73Cq6J85/fi_workdir/microH.dat /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.MY73Cq6J85 --json_outfile /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.MY73Cq6J85 --json_outfile /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3
Running: touch /tmp/nxf.MY73Cq6J85/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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.MY73Cq6J85/ctat_genome_lib_build_dir > /tmp/nxf.MY73Cq6J85/786-O_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.MY73Cq6J85/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory