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/34/51db993b97e0852cf8d02b02163edf/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/51db993b97e0852cf8d02b02163edf/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/5215cab8fcb40c871e4e37fa7dd684/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/9ff377aead2659a92d01fdb5908eba/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/9ff377aead2659a92d01fdb5908eba/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_2.fusionreport.tsv --gtf /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --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 A673_FFPE_RNA_0001_B23LG7FLT4_2.fusionreport.tsv --gtf /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/cytoBand.txt
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed
-parsing GTF file: /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2.star --out_dir /tmp/nxf.7E4AVD1Zcz/fi_workdir --reads "/tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
May 28 23:26:18 ..... started STAR run
May 28 23:26:18 ..... loading genome
May 28 23:28:08 ... generating Suffix Array index
May 28 23:32:12 ... completed Suffix Array index
May 28 23:32:12 ..... processing annotations GTF
May 28 23:32:13 ..... inserting junctions into the genome indices
May 28 23:33:14 ..... started mapping
May 29 00:20:37 ..... finished mapping
May 29 00:20:38 ..... started sorting BAM
May 29 00:20:40 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam
Execution Time = 54.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2.star --out_dir /tmp/nxf.7E4AVD1Zcz/fi_workdir --reads "/tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --remove_dups
00:21:04 : INFO : Done.
Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf
-parsing /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam
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[3810000] -done parsing /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 33845,
'exons hit < 2' => 16,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 299,
'excessive soft clipping' => 26062,
'seq-similar region overlap' => 1042,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 52,
'small anchor length' => 205,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 52,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 19,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 110,
'low complexity anchor region' => 29,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 196,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 9,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 55,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 905,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 220,
'per_id < 96' => 24725,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 36,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 16,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 857,
'num genes matched < 2' => 7,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1920
};
-writing fusion junction support info.
Execution Time = 2.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[822000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
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[59000] -fusion SPANNING read extraction for scaff: LINC00221--SPG7
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[99000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[125000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[123000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[109000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[101000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[1000]
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[116000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[114000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[79000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[34000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
[1000]
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[26000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[72000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[94000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[33000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[35000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[45000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 216380,
'lacks exon overlap' => 30430
};
Execution Time = 5.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -17999.726985
EM: Round [1] log likelihood: -17988.336901
EM: Round [2] log likelihood: -17986.049675
EM: Round [3] log likelihood: -17984.192319
EM: Round [4] log likelihood: -17982.567191
EM: Round [5] log likelihood: -17981.130734
EM: Round [6] log likelihood: -17979.854442
EM: Round [7] log likelihood: -17978.715431
EM: Round [8] log likelihood: -17977.694829
EM: Round [9] log likelihood: -17976.776904
EM: Round [10] log likelihood: -17975.948436
EM: Round [11] log likelihood: -17975.198238
EM: Round [12] log likelihood: -17974.516782
EM: Round [13] log likelihood: -17973.895910
EM: Round [14] log likelihood: -17973.328602
EM: Round [15] log likelihood: -17972.808788
EM: Round [16] log likelihood: -17972.331204
EM: Round [17] log likelihood: -17971.891262
EM: Round [18] log likelihood: -17971.484957
EM: Round [19] log likelihood: -17971.108776
EM: Round [20] log likelihood: -17970.759636
EM: Round [21] log likelihood: -17970.434820
EM: Round [22] log likelihood: -17970.131929
EM: Round [23] log likelihood: -17969.848842
EM: Round [24] log likelihood: -17969.583680
EM: Round [25] log likelihood: -17969.334773
EM: Round [26] log likelihood: -17969.100636
EM: Round [27] log likelihood: -17968.879946
EM: Round [28] log likelihood: -17968.671523
EM: Round [29] log likelihood: -17968.474314
EM: Round [30] log likelihood: -17968.287373
EM: Round [31] log likelihood: -17968.109854
EM: Round [32] log likelihood: -17967.940999
EM: Round [33] log likelihood: -17967.780125
EM: Round [34] log likelihood: -17967.626618
EM: Round [35] log likelihood: -17967.479924
EM: Round [36] log likelihood: -17967.339544
EM: Round [37] log likelihood: -17967.205024
EM: Round [38] log likelihood: -17967.075958
EM: Round [39] log likelihood: -17966.951973
EM: Round [40] log likelihood: -17966.832733
EM: Round [41] log likelihood: -17966.717932
EM: Round [42] log likelihood: -17966.607290
EM: Round [43] log likelihood: -17966.500554
EM: Round [44] log likelihood: -17966.397490
EM: Round [45] log likelihood: -17966.297885
EM: Round [46] log likelihood: -17966.201545
EM: Round [47] log likelihood: -17966.108289
EM: Round [48] log likelihood: -17966.017953
EM: Round [49] log likelihood: -17965.930384
EM: Round [50] log likelihood: -17965.845442
EM: Round [51] log likelihood: -17965.762996
EM: Round [52] log likelihood: -17965.682926
EM: Round [53] log likelihood: -17965.605120
EM: Round [54] log likelihood: -17965.529475
EM: Round [55] log likelihood: -17965.455891
EM: Round [56] log likelihood: -17965.384280
EM: Round [57] log likelihood: -17965.314557
EM: Round [58] log likelihood: -17965.246641
EM: Round [59] log likelihood: -17965.180459
EM: Round [60] log likelihood: -17965.115941
EM: Round [61] log likelihood: -17965.053020
EM: Round [62] log likelihood: -17964.991635
EM: Round [63] log likelihood: -17964.931727
EM: Round [64] log likelihood: -17964.873241
EM: Round [65] log likelihood: -17964.816124
EM: Round [66] log likelihood: -17964.760326
EM: Round [67] log likelihood: -17964.705800
EM: Round [68] log likelihood: -17964.652502
EM: Round [69] log likelihood: -17964.600389
EM: Round [70] log likelihood: -17964.549419
EM: Round [71] log likelihood: -17964.499555
EM: Round [72] log likelihood: -17964.450759
EM: Round [73] log likelihood: -17964.402997
EM: Round [74] log likelihood: -17964.356234
EM: Round [75] log likelihood: -17964.310438
EM: Round [76] log likelihood: -17964.265578
EM: Round [77] log likelihood: -17964.221625
EM: Round [78] log likelihood: -17964.178550
EM: Round [79] log likelihood: -17964.136327
EM: Round [80] log likelihood: -17964.094928
EM: Round [81] log likelihood: -17964.054329
EM: Round [82] log likelihood: -17964.014506
EM: Round [83] log likelihood: -17963.975436
EM: Round [84] log likelihood: -17963.937096
EM: Round [85] log likelihood: -17963.899465
EM: Round [86] log likelihood: -17963.862523
EM: Round [87] log likelihood: -17963.826249
EM: Round [88] log likelihood: -17963.790624
EM: Round [89] log likelihood: -17963.755630
EM: Round [90] log likelihood: -17963.721249
EM: Round [91] log likelihood: -17963.687465
EM: Round [92] log likelihood: -17963.654259
EM: Round [93] log likelihood: -17963.621618
EM: Round [94] log likelihood: -17963.589525
EM: Round [95] log likelihood: -17963.557965
EM: Round [96] log likelihood: -17963.526924
EM: Round [97] log likelihood: -17963.496388
EM: Round [98] log likelihood: -17963.466345
EM: Round [99] log likelihood: -17963.436780
EM: Round [100] log likelihood: -17963.407683
EM: Round [101] log likelihood: -17963.379039
EM: Round [102] log likelihood: -17963.350839
EM: Round [103] log likelihood: -17963.323071
EM: Round [104] log likelihood: -17963.295723
EM: Round [105] log likelihood: -17963.268786
EM: Round [106] log likelihood: -17963.242249
EM: Round [107] log likelihood: -17963.216103
EM: Round [108] log likelihood: -17963.190337
EM: Round [109] log likelihood: -17963.164944
EM: Round [110] log likelihood: -17963.139913
EM: Round [111] log likelihood: -17963.115236
EM: Round [112] log likelihood: -17963.090906
EM: Round [113] log likelihood: -17963.066913
EM: Round [114] log likelihood: -17963.043251
EM: Round [115] log likelihood: -17963.019911
EM: Round [116] log likelihood: -17962.996886
EM: Round [117] log likelihood: -17962.974170
EM: Round [118] log likelihood: -17962.951755
EM: Round [119] log likelihood: -17962.929634
EM: Round [120] log likelihood: -17962.907802
EM: Round [121] log likelihood: -17962.886251
EM: Round [122] log likelihood: -17962.864977
EM: Round [123] log likelihood: -17962.843972
EM: Round [124] log likelihood: -17962.823232
EM: Round [125] log likelihood: -17962.802751
EM: Round [126] log likelihood: -17962.782523
EM: Round [127] log likelihood: -17962.762544
EM: Round [128] log likelihood: -17962.742808
EM: Round [129] log likelihood: -17962.723310
EM: Round [130] log likelihood: -17962.704045
EM: Round [131] log likelihood: -17962.685010
EM: Round [132] log likelihood: -17962.666199
EM: Round [133] log likelihood: -17962.647608
EM: Round [134] log likelihood: -17962.629233
EM: Round [135] log likelihood: -17962.611070
EM: Round [136] log likelihood: -17962.593115
EM: Round [137] log likelihood: -17962.575364
EM: Round [138] log likelihood: -17962.557813
EM: Round [139] log likelihood: -17962.540458
EM: Round [140] log likelihood: -17962.523297
EM: Round [141] log likelihood: -17962.506325
EM: Round [142] log likelihood: -17962.489538
EM: Round [143] log likelihood: -17962.472935
EM: Round [144] log likelihood: -17962.456512
EM: Round [145] log likelihood: -17962.440265
EM: Round [146] log likelihood: -17962.424191
EM: Round [147] log likelihood: -17962.408288
EM: Round [148] log likelihood: -17962.392552
EM: Round [149] log likelihood: -17962.376982
EM: Round [150] log likelihood: -17962.361573
EM: Round [151] log likelihood: -17962.346324
EM: Round [152] log likelihood: -17962.331232
EM: Round [153] log likelihood: -17962.316295
EM: Round [154] log likelihood: -17962.301509
EM: Round [155] log likelihood: -17962.286873
EM: Round [156] log likelihood: -17962.272383
EM: Round [157] log likelihood: -17962.258039
EM: Round [158] log likelihood: -17962.243837
EM: Round [159] log likelihood: -17962.229776
EM: Round [160] log likelihood: -17962.215853
EM: Round [161] log likelihood: -17962.202066
EM: Round [162] log likelihood: -17962.188414
EM: Round [163] log likelihood: -17962.174894
EM: Round [164] log likelihood: -17962.161504
EM: Round [165] log likelihood: -17962.148242
EM: Round [166] log likelihood: -17962.135107
EM: Round [167] log likelihood: -17962.122097
EM: Round [168] log likelihood: -17962.109209
EM: Round [169] log likelihood: -17962.096443
EM: Round [170] log likelihood: -17962.083796
EM: Round [171] log likelihood: -17962.071267
EM: Round [172] log likelihood: -17962.058855
EM: Round [173] log likelihood: -17962.046557
EM: Round [174] log likelihood: -17962.034372
EM: Round [175] log likelihood: -17962.022299
EM: Round [176] log likelihood: -17962.010336
EM: Round [177] log likelihood: -17961.998481
EM: Round [178] log likelihood: -17961.986734
EM: Round [179] log likelihood: -17961.975092
EM: Round [180] log likelihood: -17961.963555
EM: Round [181] log likelihood: -17961.952121
EM: Round [182] log likelihood: -17961.940789
EM: Round [183] log likelihood: -17961.929557
EM: Round [184] log likelihood: -17961.918424
EM: Round [185] log likelihood: -17961.907390
EM: Round [186] log likelihood: -17961.896452
EM: Round [187] log likelihood: -17961.885609
EM: Round [188] log likelihood: -17961.874861
EM: Round [189] log likelihood: -17961.864206
EM: Round [190] log likelihood: -17961.853643
EM: Round [191] log likelihood: -17961.843171
EM: Round [192] log likelihood: -17961.832788
EM: Round [193] log likelihood: -17961.822495
EM: Round [194] log likelihood: -17961.812289
EM: Round [195] log likelihood: -17961.802170
EM: Round [196] log likelihood: -17961.792137
EM: Round [197] log likelihood: -17961.782188
EM: Round [198] log likelihood: -17961.772323
EM: Round [199] log likelihood: -17961.762540
EM: Round [200] log likelihood: -17961.752839
EM: Round [201] log likelihood: -17961.743219
EM: Round [202] log likelihood: -17961.733679
EM: Round [203] log likelihood: -17961.724218
EM: Round [204] log likelihood: -17961.714835
EM: Round [205] log likelihood: -17961.705530
EM: Round [206] log likelihood: -17961.696300
EM: Round [207] log likelihood: -17961.687146
EM: Round [208] log likelihood: -17961.678067
EM: Round [209] log likelihood: -17961.669062
EM: Round [210] log likelihood: -17961.660130
EM: Round [211] log likelihood: -17961.651270
EM: Round [212] log likelihood: -17961.642481
EM: Round [213] log likelihood: -17961.633763
EM: Round [214] log likelihood: -17961.625115
EM: Round [215] log likelihood: -17961.616536
EM: Round [216] log likelihood: -17961.608026
EM: Round [217] log likelihood: -17961.599584
EM: Round [218] log likelihood: -17961.591208
EM: Round [219] log likelihood: -17961.582899
EM: Round [220] log likelihood: -17961.574655
EM: Round [221] log likelihood: -17961.566476
EM: Round [222] log likelihood: -17961.558362
EM: Round [223] log likelihood: -17961.550311
EM: Round [224] log likelihood: -17961.542323
EM: Round [225] log likelihood: -17961.534398
EM: Round [226] log likelihood: -17961.526534
EM: Round [227] log likelihood: -17961.518731
EM: Round [228] log likelihood: -17961.510988
EM: Round [229] log likelihood: -17961.503305
EM: Round [230] log likelihood: -17961.495682
EM: Round [231] log likelihood: -17961.488117
EM: Round [232] log likelihood: -17961.480610
EM: Round [233] log likelihood: -17961.473161
EM: Round [234] log likelihood: -17961.465768
EM: Round [235] log likelihood: -17961.458432
EM: Round [236] log likelihood: -17961.451151
EM: Round [237] log likelihood: -17961.443926
EM: Round [238] log likelihood: -17961.436755
EM: Round [239] log likelihood: -17961.429639
EM: Round [240] log likelihood: -17961.422576
EM: Round [241] log likelihood: -17961.415566
EM: Round [242] log likelihood: -17961.408609
EM: Round [243] log likelihood: -17961.401704
EM: Round [244] log likelihood: -17961.394850
EM: Round [245] log likelihood: -17961.388048
EM: Round [246] log likelihood: -17961.381296
EM: Round [247] log likelihood: -17961.374594
EM: Round [248] log likelihood: -17961.367942
EM: Round [249] log likelihood: -17961.361339
EM: Round [250] log likelihood: -17961.354784
EM: Round [251] log likelihood: -17961.348278
EM: Round [252] log likelihood: -17961.341820
EM: Round [253] log likelihood: -17961.335409
EM: Round [254] log likelihood: -17961.329045
EM: Round [255] log likelihood: -17961.322727
EM: Round [256] log likelihood: -17961.316456
EM: Round [257] log likelihood: -17961.310230
EM: Round [258] log likelihood: -17961.304049
EM: Round [259] log likelihood: -17961.297913
EM: Round [260] log likelihood: -17961.291822
EM: Round [261] log likelihood: -17961.285774
EM: Round [262] log likelihood: -17961.279770
EM: Round [263] log likelihood: -17961.273809
EM: Round [264] log likelihood: -17961.267891
EM: Round [265] log likelihood: -17961.262015
EM: Round [266] log likelihood: -17961.256181
EM: Round [267] log likelihood: -17961.250389
EM: Round [268] log likelihood: -17961.244638
EM: Round [269] log likelihood: -17961.238928
EM: Round [270] log likelihood: -17961.233258
EM: Round [271] log likelihood: -17961.227629
EM: Round [272] log likelihood: -17961.222040
EM: Round [273] log likelihood: -17961.216489
EM: Round [274] log likelihood: -17961.210978
EM: Round [275] log likelihood: -17961.205506
EM: Round [276] log likelihood: -17961.200072
EM: Round [277] log likelihood: -17961.194676
EM: Round [278] log likelihood: -17961.189318
EM: Round [279] log likelihood: -17961.183998
EM: Round [280] log likelihood: -17961.178714
EM: Round [281] log likelihood: -17961.173467
EM: Round [282] log likelihood: -17961.168257
EM: Round [283] log likelihood: -17961.163083
EM: Round [284] log likelihood: -17961.157944
EM: Round [285] log likelihood: -17961.152841
EM: Round [286] log likelihood: -17961.147773
EM: Round [287] log likelihood: -17961.142740
EM: Round [288] log likelihood: -17961.137742
EM: Round [289] log likelihood: -17961.132778
EM: Round [290] log likelihood: -17961.127848
EM: Round [291] log likelihood: -17961.122952
EM: Round [292] log likelihood: -17961.118089
EM: Round [293] log likelihood: -17961.113259
EM: Round [294] log likelihood: -17961.108462
EM: Round [295] log likelihood: -17961.103698
EM: Round [296] log likelihood: -17961.098966
EM: Round [297] log likelihood: -17961.094266
EM: Round [298] log likelihood: -17961.089598
EM: Round [299] log likelihood: -17961.084962
EM: Round [300] log likelihood: -17961.080356
EM: Round [301] log likelihood: -17961.075782
EM: Round [302] log likelihood: -17961.071238
EM: Round [303] log likelihood: -17961.066725
EM: Round [304] log likelihood: -17961.062242
EM: Round [305] log likelihood: -17961.057788
EM: Round [306] log likelihood: -17961.053365
EM: Round [307] log likelihood: -17961.048971
EM: Round [308] log likelihood: -17961.044606
EM: Round [309] log likelihood: -17961.040271
EM: Round [310] log likelihood: -17961.035964
EM: Round [311] log likelihood: -17961.031685
EM: Round [312] log likelihood: -17961.027435
EM: Round [313] log likelihood: -17961.023213
EM: Round [314] log likelihood: -17961.019019
EM: Round [315] log likelihood: -17961.014852
EM: Round [316] log likelihood: -17961.010712
EM: Round [317] log likelihood: -17961.006600
EM: Round [318] log likelihood: -17961.002515
EM: Round [319] log likelihood: -17960.998456
EM: Round [320] log likelihood: -17960.994424
EM: Round [321] log likelihood: -17960.990418
EM: Round [322] log likelihood: -17960.986438
EM: Round [323] log likelihood: -17960.982485
EM: Round [324] log likelihood: -17960.978556
EM: Round [325] log likelihood: -17960.974653
EM: Round [326] log likelihood: -17960.970776
EM: Round [327] log likelihood: -17960.966923
EM: Round [328] log likelihood: -17960.963095
EM: Round [329] log likelihood: -17960.959292
EM: Round [330] log likelihood: -17960.955514
EM: Round [331] log likelihood: -17960.951759
EM: Round [332] log likelihood: -17960.948029
EM: Round [333] log likelihood: -17960.944322
EM: Round [334] log likelihood: -17960.940640
EM: Round [335] log likelihood: -17960.936980
EM: Round [336] log likelihood: -17960.933344
EM: Round [337] log likelihood: -17960.929731
EM: Round [338] log likelihood: -17960.926142
EM: Round [339] log likelihood: -17960.922574
EM: Round [340] log likelihood: -17960.919030
EM: Round [341] log likelihood: -17960.915508
EM: Round [342] log likelihood: -17960.912008
EM: Round [343] log likelihood: -17960.908530
EM: Round [344] log likelihood: -17960.905074
EM: Round [345] log likelihood: -17960.901640
EM: Round [346] log likelihood: -17960.898227
EM: Round [347] log likelihood: -17960.894836
EM: Round [348] log likelihood: -17960.891465
EM: Round [349] log likelihood: -17960.888116
EM: Round [350] log likelihood: -17960.884788
EM: Round [351] log likelihood: -17960.881481
EM: Round [352] log likelihood: -17960.878194
EM: Round [353] log likelihood: -17960.874928
EM: Round [354] log likelihood: -17960.871682
EM: Round [355] log likelihood: -17960.868456
EM: Round [356] log likelihood: -17960.865249
EM: Round [357] log likelihood: -17960.862063
EM: Round [358] log likelihood: -17960.858897
EM: Round [359] log likelihood: -17960.855749
EM: Round [360] log likelihood: -17960.852622
EM: Round [361] log likelihood: -17960.849513
EM: Round [362] log likelihood: -17960.846424
EM: Round [363] log likelihood: -17960.843353
EM: Round [364] log likelihood: -17960.840301
EM: Round [365] log likelihood: -17960.837268
EM: Round [366] log likelihood: -17960.834253
EM: Round [367] log likelihood: -17960.831257
EM: Round [368] log likelihood: -17960.828279
EM: Round [369] log likelihood: -17960.825319
EM: Round [370] log likelihood: -17960.822377
EM: Round [371] log likelihood: -17960.819453
EM: Round [372] log likelihood: -17960.816546
EM: Round [373] log likelihood: -17960.813657
EM: Round [374] log likelihood: -17960.810785
EM: Round [375] log likelihood: -17960.807931
EM: Round [376] log likelihood: -17960.805094
EM: Round [377] log likelihood: -17960.802274
EM: Round [378] log likelihood: -17960.799470
EM: Round [379] log likelihood: -17960.796684
EM: Round [380] log likelihood: -17960.793914
EM: Round [381] log likelihood: -17960.791161
EM: Round [382] log likelihood: -17960.788424
EM: Round [383] log likelihood: -17960.785703
EM: Round [384] log likelihood: -17960.782999
EM: Round [385] log likelihood: -17960.780311
EM: Round [386] log likelihood: -17960.777638
EM: Round [387] log likelihood: -17960.774982
EM: Round [388] log likelihood: -17960.772341
EM: Round [389] log likelihood: -17960.769716
EM: Round [390] log likelihood: -17960.767106
EM: Round [391] log likelihood: -17960.764511
EM: Round [392] log likelihood: -17960.761932
EM: Round [393] log likelihood: -17960.759368
EM: Round [394] log likelihood: -17960.756819
EM: Round [395] log likelihood: -17960.754285
EM: Round [396] log likelihood: -17960.751765
EM: Round [397] log likelihood: -17960.749261
EM: Round [398] log likelihood: -17960.746771
EM: Round [399] log likelihood: -17960.744295
EM: Round [400] log likelihood: -17960.741834
EM: Round [401] log likelihood: -17960.739387
EM: Round [402] log likelihood: -17960.736955
EM: Round [403] log likelihood: -17960.734536
EM: Round [404] log likelihood: -17960.732131
EM: Round [405] log likelihood: -17960.729741
EM: Round [406] log likelihood: -17960.727364
EM: Round [407] log likelihood: -17960.725000
EM: Round [408] log likelihood: -17960.722651
EM: Round [409] log likelihood: -17960.720315
EM: Round [410] log likelihood: -17960.717992
EM: Round [411] log likelihood: -17960.715682
EM: Round [412] log likelihood: -17960.713386
EM: Round [413] log likelihood: -17960.711103
EM: Round [414] log likelihood: -17960.708833
EM: Round [415] log likelihood: -17960.706575
EM: Round [416] log likelihood: -17960.704331
EM: Round [417] log likelihood: -17960.702099
EM: Round [418] log likelihood: -17960.699880
EM: Round [419] log likelihood: -17960.697674
EM: Round [420] log likelihood: -17960.695480
EM: Round [421] log likelihood: -17960.693298
EM: Round [422] log likelihood: -17960.691129
EM: Round [423] log likelihood: -17960.688972
EM: Round [424] log likelihood: -17960.686827
EM: Round [425] log likelihood: -17960.684694
EM: Round [426] log likelihood: -17960.682573
EM: Round [427] log likelihood: -17960.680464
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EM: Round [887] log likelihood: -17960.287654
EM: Round [888] log likelihood: -17960.287342
EM: Round [889] log likelihood: -17960.287031
EM: Round [890] log likelihood: -17960.286721
EM: Round [891] log likelihood: -17960.286412
EM: Round [892] log likelihood: -17960.286105
EM: Round [893] log likelihood: -17960.285797
EM: Round [894] log likelihood: -17960.285491
EM: Round [895] log likelihood: -17960.285186
EM: Round [896] log likelihood: -17960.284882
EM: Round [897] log likelihood: -17960.284579
EM: Round [898] log likelihood: -17960.284276
EM: Round [899] log likelihood: -17960.283975
EM: Round [900] log likelihood: -17960.283674
EM: Round [901] log likelihood: -17960.283374
EM: Round [902] log likelihood: -17960.283075
EM: Round [903] log likelihood: -17960.282778
EM: Round [904] log likelihood: -17960.282481
EM: Round [905] log likelihood: -17960.282184
EM: Round [906] log likelihood: -17960.281889
EM: Round [907] log likelihood: -17960.281595
EM: Round [908] log likelihood: -17960.281301
EM: Round [909] log likelihood: -17960.281009
EM: Round [910] log likelihood: -17960.280717
EM: Round [911] log likelihood: -17960.280426
EM: Round [912] log likelihood: -17960.280136
EM: Round [913] log likelihood: -17960.279847
EM: Round [914] log likelihood: -17960.279558
EM: Round [915] log likelihood: -17960.279271
EM: Round [916] log likelihood: -17960.278984
EM: Round [917] log likelihood: -17960.278699
EM: Round [918] log likelihood: -17960.278414
EM: Round [919] log likelihood: -17960.278130
EM: Round [920] log likelihood: -17960.277846
EM: Round [921] log likelihood: -17960.277564
EM: Round [922] log likelihood: -17960.277282
EM: Round [923] log likelihood: -17960.277002
EM: Round [924] log likelihood: -17960.276722
EM: Round [925] log likelihood: -17960.276443
EM: Round [926] log likelihood: -17960.276164
EM: Round [927] log likelihood: -17960.275887
EM: Round [928] log likelihood: -17960.275610
EM: Round [929] log likelihood: -17960.275334
EM: Round [930] log likelihood: -17960.275059
EM: Round [931] log likelihood: -17960.274785
EM: Round [932] log likelihood: -17960.274512
EM: Round [933] log likelihood: -17960.274239
EM: Round [934] log likelihood: -17960.273967
EM: Round [935] log likelihood: -17960.273696
EM: Round [936] log likelihood: -17960.273426
EM: Round [937] log likelihood: -17960.273156
EM: Round [938] log likelihood: -17960.272888
EM: Round [939] log likelihood: -17960.272620
EM: Round [940] log likelihood: -17960.272353
EM: Round [941] log likelihood: -17960.272086
EM: Round [942] log likelihood: -17960.271821
EM: Round [943] log likelihood: -17960.271556
EM: Round [944] log likelihood: -17960.271292
EM: Round [945] log likelihood: -17960.271028
EM: Round [946] log likelihood: -17960.270766
EM: Round [947] log likelihood: -17960.270504
EM: Round [948] log likelihood: -17960.270243
EM: Round [949] log likelihood: -17960.269983
EM: Round [950] log likelihood: -17960.269723
EM: Round [951] log likelihood: -17960.269464
EM: Round [952] log likelihood: -17960.269206
EM: Round [953] log likelihood: -17960.268949
EM: Round [954] log likelihood: -17960.268692
EM: Round [955] log likelihood: -17960.268436
EM: Round [956] log likelihood: -17960.268181
EM: Round [957] log likelihood: -17960.267927
EM: Round [958] log likelihood: -17960.267673
EM: Round [959] log likelihood: -17960.267420
EM: Round [960] log likelihood: -17960.267168
EM: Round [961] log likelihood: -17960.266916
EM: Round [962] log likelihood: -17960.266666
EM: Round [963] log likelihood: -17960.266415
EM: Round [964] log likelihood: -17960.266166
EM: Round [965] log likelihood: -17960.265917
EM: Round [966] log likelihood: -17960.265669
EM: Round [967] log likelihood: -17960.265422
EM: Round [968] log likelihood: -17960.265176
EM: Round [969] log likelihood: -17960.264930
EM: Round [970] log likelihood: -17960.264684
EM: Round [971] log likelihood: -17960.264440
EM: Round [972] log likelihood: -17960.264196
EM: Round [973] log likelihood: -17960.263953
EM: Round [974] log likelihood: -17960.263711
EM: Round [975] log likelihood: -17960.263469
EM: Round [976] log likelihood: -17960.263228
EM: Round [977] log likelihood: -17960.262987
EM: Round [978] log likelihood: -17960.262748
EM: Round [979] log likelihood: -17960.262509
EM: Round [980] log likelihood: -17960.262270
EM: Round [981] log likelihood: -17960.262032
EM: Round [982] log likelihood: -17960.261795
EM: Round [983] log likelihood: -17960.261559
EM: Round [984] log likelihood: -17960.261323
EM: Round [985] log likelihood: -17960.261088
EM: Round [986] log likelihood: -17960.260854
EM: Round [987] log likelihood: -17960.260620
EM: Round [988] log likelihood: -17960.260387
EM: Round [989] log likelihood: -17960.260154
EM: Round [990] log likelihood: -17960.259922
EM: Round [991] log likelihood: -17960.259691
EM: Round [992] log likelihood: -17960.259461
EM: Round [993] log likelihood: -17960.259231
EM: Round [994] log likelihood: -17960.259002
EM: Round [995] log likelihood: -17960.258773
EM: Round [996] log likelihood: -17960.258545
EM: Round [997] log likelihood: -17960.258318
EM: Round [998] log likelihood: -17960.258091
EM: Round [999] log likelihood: -17960.257865
EM: Round [1000] log likelihood: -17960.257639
EM: Round [1001] log likelihood: -17960.257414
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam into /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir
-done, see /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -9990.462536
EM: Round [1] log likelihood: -9988.004857
EM: Round [2] log likelihood: -9988.002557
EM: Round [3] log likelihood: -9988.000372
EM: Round [4] log likelihood: -9987.998196
EM: Round [5] log likelihood: -9987.996029
EM: Round [6] log likelihood: -9987.993872
EM: Round [7] log likelihood: -9987.991724
EM: Round [8] log likelihood: -9987.989586
EM: Round [9] log likelihood: -9987.987457
EM: Round [10] log likelihood: -9987.985337
EM: Round [11] log likelihood: -9987.983227
EM: Round [12] log likelihood: -9987.981125
EM: Round [13] log likelihood: -9987.979033
EM: Round [14] log likelihood: -9987.976949
EM: Round [15] log likelihood: -9987.974875
EM: Round [16] log likelihood: -9987.972809
EM: Round [17] log likelihood: -9987.970752
EM: Round [18] log likelihood: -9987.968704
EM: Round [19] log likelihood: -9987.966665
EM: Round [20] log likelihood: -9987.964634
EM: Round [21] log likelihood: -9987.962612
EM: Round [22] log likelihood: -9987.960598
EM: Round [23] log likelihood: -9987.958593
EM: Round [24] log likelihood: -9987.956597
EM: Round [25] log likelihood: -9987.954609
EM: Round [26] log likelihood: -9987.952629
EM: Round [27] log likelihood: -9987.950657
EM: Round [28] log likelihood: -9987.948694
EM: Round [29] log likelihood: -9987.946739
EM: Round [30] log likelihood: -9987.944792
EM: Round [31] log likelihood: -9987.942853
EM: Round [32] log likelihood: -9987.940922
EM: Round [33] log likelihood: -9987.938999
EM: Round [34] log likelihood: -9987.937084
EM: Round [35] log likelihood: -9987.935177
EM: Round [36] log likelihood: -9987.933278
EM: Round [37] log likelihood: -9987.931387
EM: Round [38] log likelihood: -9987.929503
EM: Round [39] log likelihood: -9987.927627
EM: Round [40] log likelihood: -9987.925759
EM: Round [41] log likelihood: -9987.923898
EM: Round [42] log likelihood: -9987.922045
EM: Round [43] log likelihood: -9987.920199
EM: Round [44] log likelihood: -9987.918361
EM: Round [45] log likelihood: -9987.916531
EM: Round [46] log likelihood: -9987.914707
EM: Round [47] log likelihood: -9987.912891
EM: Round [48] log likelihood: -9987.911083
EM: Round [49] log likelihood: -9987.909282
EM: Round [50] log likelihood: -9987.907487
EM: Round [51] log likelihood: -9987.905700
EM: Round [52] log likelihood: -9987.903921
EM: Round [53] log likelihood: -9987.902148
EM: Round [54] log likelihood: -9987.900382
EM: Round [55] log likelihood: -9987.898624
EM: Round [56] log likelihood: -9987.896872
EM: Round [57] log likelihood: -9987.895127
EM: Round [58] log likelihood: -9987.893390
EM: Round [59] log likelihood: -9987.891659
EM: Round [60] log likelihood: -9987.889934
EM: Round [61] log likelihood: -9987.888217
EM: Round [62] log likelihood: -9987.886507
EM: Round [63] log likelihood: -9987.884803
EM: Round [64] log likelihood: -9987.883105
EM: Round [65] log likelihood: -9987.881415
EM: Round [66] log likelihood: -9987.879731
EM: Round [67] log likelihood: -9987.878053
EM: Round [68] log likelihood: -9987.876382
EM: Round [69] log likelihood: -9987.874718
EM: Round [70] log likelihood: -9987.873060
EM: Round [71] log likelihood: -9987.871408
EM: Round [72] log likelihood: -9987.869763
EM: Round [73] log likelihood: -9987.868124
EM: Round [74] log likelihood: -9987.866492
EM: Round [75] log likelihood: -9987.864865
EM: Round [76] log likelihood: -9987.863245
EM: Round [77] log likelihood: -9987.861631
EM: Round [78] log likelihood: -9987.860024
EM: Round [79] log likelihood: -9987.858422
EM: Round [80] log likelihood: -9987.856827
EM: Round [81] log likelihood: -9987.855237
EM: Round [82] log likelihood: -9987.853654
EM: Round [83] log likelihood: -9987.852077
EM: Round [84] log likelihood: -9987.850505
EM: Round [85] log likelihood: -9987.848940
EM: Round [86] log likelihood: -9987.847380
EM: Round [87] log likelihood: -9987.845827
EM: Round [88] log likelihood: -9987.844279
EM: Round [89] log likelihood: -9987.842737
EM: Round [90] log likelihood: -9987.841201
EM: Round [91] log likelihood: -9987.839670
EM: Round [92] log likelihood: -9987.838145
EM: Round [93] log likelihood: -9987.836626
EM: Round [94] log likelihood: -9987.835113
EM: Round [95] log likelihood: -9987.833605
EM: Round [96] log likelihood: -9987.832103
EM: Round [97] log likelihood: -9987.830607
EM: Round [98] log likelihood: -9987.829116
EM: Round [99] log likelihood: -9987.827630
EM: Round [100] log likelihood: -9987.826150
EM: Round [101] log likelihood: -9987.824676
EM: Round [102] log likelihood: -9987.823207
EM: Round [103] log likelihood: -9987.821743
EM: Round [104] log likelihood: -9987.820285
EM: Round [105] log likelihood: -9987.818832
EM: Round [106] log likelihood: -9987.817384
EM: Round [107] log likelihood: -9987.815942
EM: Round [108] log likelihood: -9987.814505
EM: Round [109] log likelihood: -9987.813073
EM: Round [110] log likelihood: -9987.811646
EM: Round [111] log likelihood: -9987.810225
EM: Round [112] log likelihood: -9987.808809
EM: Round [113] log likelihood: -9987.807397
EM: Round [114] log likelihood: -9987.805991
EM: Round [115] log likelihood: -9987.804590
EM: Round [116] log likelihood: -9987.803195
EM: Round [117] log likelihood: -9987.801804
EM: Round [118] log likelihood: -9987.800418
EM: Round [119] log likelihood: -9987.799037
EM: Round [120] log likelihood: -9987.797661
EM: Round [121] log likelihood: -9987.796290
EM: Round [122] log likelihood: -9987.794924
EM: Round [123] log likelihood: -9987.793563
EM: Round [124] log likelihood: -9987.792207
EM: Round [125] log likelihood: -9987.790855
EM: Round [126] log likelihood: -9987.789509
EM: Round [127] log likelihood: -9987.788167
EM: Round [128] log likelihood: -9987.786830
EM: Round [129] log likelihood: -9987.785498
EM: Round [130] log likelihood: -9987.784170
EM: Round [131] log likelihood: -9987.782847
EM: Round [132] log likelihood: -9987.781529
EM: Round [133] log likelihood: -9987.780215
EM: Round [134] log likelihood: -9987.778906
EM: Round [135] log likelihood: -9987.777602
EM: Round [136] log likelihood: -9987.776302
EM: Round [137] log likelihood: -9987.775007
EM: Round [138] log likelihood: -9987.773716
EM: Round [139] log likelihood: -9987.772430
EM: Round [140] log likelihood: -9987.771148
EM: Round [141] log likelihood: -9987.769871
EM: Round [142] log likelihood: -9987.768599
EM: Round [143] log likelihood: -9987.767330
EM: Round [144] log likelihood: -9987.766066
EM: Round [145] log likelihood: -9987.764807
EM: Round [146] log likelihood: -9987.763552
EM: Round [147] log likelihood: -9987.762301
EM: Round [148] log likelihood: -9987.761055
EM: Round [149] log likelihood: -9987.759813
EM: Round [150] log likelihood: -9987.758575
EM: Round [151] log likelihood: -9987.757341
EM: Round [152] log likelihood: -9987.756112
EM: Round [153] log likelihood: -9987.754887
EM: Round [154] log likelihood: -9987.753666
EM: Round [155] log likelihood: -9987.752449
EM: Round [156] log likelihood: -9987.751237
EM: Round [157] log likelihood: -9987.750029
EM: Round [158] log likelihood: -9987.748824
EM: Round [159] log likelihood: -9987.747624
EM: Round [160] log likelihood: -9987.746428
EM: Round [161] log likelihood: -9987.745236
EM: Round [162] log likelihood: -9987.744049
EM: Round [163] log likelihood: -9987.742865
EM: Round [164] log likelihood: -9987.741685
EM: Round [165] log likelihood: -9987.740509
EM: Round [166] log likelihood: -9987.739337
EM: Round [167] log likelihood: -9987.738169
EM: Round [168] log likelihood: -9987.737005
EM: Round [169] log likelihood: -9987.735846
EM: Round [170] log likelihood: -9987.734689
EM: Round [171] log likelihood: -9987.733537
EM: Round [172] log likelihood: -9987.732389
EM: Round [173] log likelihood: -9987.731245
EM: Round [174] log likelihood: -9987.730104
EM: Round [175] log likelihood: -9987.728967
EM: Round [176] log likelihood: -9987.727834
EM: Round [177] log likelihood: -9987.726705
EM: Round [178] log likelihood: -9987.725580
EM: Round [179] log likelihood: -9987.724458
EM: Round [180] log likelihood: -9987.723340
EM: Round [181] log likelihood: -9987.722226
EM: Round [182] log likelihood: -9987.721115
EM: Round [183] log likelihood: -9987.720009
EM: Round [184] log likelihood: -9987.718906
EM: Round [185] log likelihood: -9987.717806
EM: Round [186] log likelihood: -9987.716710
EM: Round [187] log likelihood: -9987.715618
EM: Round [188] log likelihood: -9987.714529
EM: Round [189] log likelihood: -9987.713444
EM: Round [190] log likelihood: -9987.712363
EM: Round [191] log likelihood: -9987.711285
EM: Round [192] log likelihood: -9987.710211
EM: Round [193] log likelihood: -9987.709140
EM: Round [194] log likelihood: -9987.708073
EM: Round [195] log likelihood: -9987.707009
EM: Round [196] log likelihood: -9987.705949
EM: Round [197] log likelihood: -9987.704892
EM: Round [198] log likelihood: -9987.703839
EM: Round [199] log likelihood: -9987.702789
EM: Round [200] log likelihood: -9987.701742
EM: Round [201] log likelihood: -9987.700699
EM: Round [202] log likelihood: -9987.699660
EM: Round [203] log likelihood: -9987.698623
EM: Round [204] log likelihood: -9987.697590
EM: Round [205] log likelihood: -9987.696561
EM: Round [206] log likelihood: -9987.695535
EM: Round [207] log likelihood: -9987.694512
EM: Round [208] log likelihood: -9987.693492
EM: Round [209] log likelihood: -9987.692476
EM: Round [210] log likelihood: -9987.691463
EM: Round [211] log likelihood: -9987.690453
EM: Round [212] log likelihood: -9987.689447
EM: Round [213] log likelihood: -9987.688443
EM: Round [214] log likelihood: -9987.687443
EM: Round [215] log likelihood: -9987.686446
EM: Round [216] log likelihood: -9987.685453
EM: Round [217] log likelihood: -9987.684462
EM: Round [218] log likelihood: -9987.683475
EM: Round [219] log likelihood: -9987.682491
EM: Round [220] log likelihood: -9987.681510
EM: Round [221] log likelihood: -9987.680532
EM: Round [222] log likelihood: -9987.679558
EM: Round [223] log likelihood: -9987.678586
EM: Round [224] log likelihood: -9987.677617
EM: Round [225] log likelihood: -9987.676652
EM: Round [226] log likelihood: -9987.675690
EM: Round [227] log likelihood: -9987.674730
EM: Round [228] log likelihood: -9987.673774
EM: Round [229] log likelihood: -9987.672821
EM: Round [230] log likelihood: -9987.671871
EM: Round [231] log likelihood: -9987.670924
EM: Round [232] log likelihood: -9987.669979
EM: Round [233] log likelihood: -9987.669038
EM: Round [234] log likelihood: -9987.668100
EM: Round [235] log likelihood: -9987.667165
EM: Round [236] log likelihood: -9987.666232
EM: Round [237] log likelihood: -9987.665303
EM: Round [238] log likelihood: -9987.664376
EM: Round [239] log likelihood: -9987.663453
EM: Round [240] log likelihood: -9987.662532
EM: Round [241] log likelihood: -9987.661614
EM: Round [242] log likelihood: -9987.660699
EM: Round [243] log likelihood: -9987.659787
EM: Round [244] log likelihood: -9987.658878
EM: Round [245] log likelihood: -9987.657972
EM: Round [246] log likelihood: -9987.657068
EM: Round [247] log likelihood: -9987.656167
EM: Round [248] log likelihood: -9987.655269
EM: Round [249] log likelihood: -9987.654374
EM: Round [250] log likelihood: -9987.653482
EM: Round [251] log likelihood: -9987.652592
EM: Round [252] log likelihood: -9987.651706
EM: Round [253] log likelihood: -9987.650821
EM: Round [254] log likelihood: -9987.649940
EM: Round [255] log likelihood: -9987.649062
EM: Round [256] log likelihood: -9987.648186
EM: Round [257] log likelihood: -9987.647312
EM: Round [258] log likelihood: -9987.646442
EM: Round [259] log likelihood: -9987.645574
EM: Round [260] log likelihood: -9987.644709
EM: Round [261] log likelihood: -9987.643847
EM: Round [262] log likelihood: -9987.642987
EM: Round [263] log likelihood: -9987.642130
EM: Round [264] log likelihood: -9987.641275
EM: Round [265] log likelihood: -9987.640423
EM: Round [266] log likelihood: -9987.639574
EM: Round [267] log likelihood: -9987.638727
EM: Round [268] log likelihood: -9987.637883
EM: Round [269] log likelihood: -9987.637042
EM: Round [270] log likelihood: -9987.636203
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EM: Round [733] log likelihood: -9987.419203
EM: Round [734] log likelihood: -9987.418962
EM: Round [735] log likelihood: -9987.418722
EM: Round [736] log likelihood: -9987.418482
EM: Round [737] log likelihood: -9987.418243
EM: Round [738] log likelihood: -9987.418004
EM: Round [739] log likelihood: -9987.417766
EM: Round [740] log likelihood: -9987.417529
EM: Round [741] log likelihood: -9987.417292
EM: Round [742] log likelihood: -9987.417055
EM: Round [743] log likelihood: -9987.416820
EM: Round [744] log likelihood: -9987.416585
EM: Round [745] log likelihood: -9987.416350
EM: Round [746] log likelihood: -9987.416116
EM: Round [747] log likelihood: -9987.415883
EM: Round [748] log likelihood: -9987.415650
EM: Round [749] log likelihood: -9987.415418
EM: Round [750] log likelihood: -9987.415186
EM: Round [751] log likelihood: -9987.414955
EM: Round [752] log likelihood: -9987.414724
EM: Round [753] log likelihood: -9987.414494
EM: Round [754] log likelihood: -9987.414265
EM: Round [755] log likelihood: -9987.414036
EM: Round [756] log likelihood: -9987.413808
EM: Round [757] log likelihood: -9987.413580
EM: Round [758] log likelihood: -9987.413353
EM: Round [759] log likelihood: -9987.413126
EM: Round [760] log likelihood: -9987.412900
EM: Round [761] log likelihood: -9987.412675
EM: Round [762] log likelihood: -9987.412450
EM: Round [763] log likelihood: -9987.412225
EM: Round [764] log likelihood: -9987.412001
EM: Round [765] log likelihood: -9987.411778
EM: Round [766] log likelihood: -9987.411555
EM: Round [767] log likelihood: -9987.411333
EM: Round [768] log likelihood: -9987.411111
EM: Round [769] log likelihood: -9987.410890
EM: Round [770] log likelihood: -9987.410669
EM: Round [771] log likelihood: -9987.410449
EM: Round [772] log likelihood: -9987.410230
EM: Round [773] log likelihood: -9987.410011
EM: Round [774] log likelihood: -9987.409792
EM: Round [775] log likelihood: -9987.409574
EM: Round [776] log likelihood: -9987.409357
EM: Round [777] log likelihood: -9987.409140
EM: Round [778] log likelihood: -9987.408924
EM: Round [779] log likelihood: -9987.408708
EM: Round [780] log likelihood: -9987.408493
EM: Round [781] log likelihood: -9987.408278
EM: Round [782] log likelihood: -9987.408064
EM: Round [783] log likelihood: -9987.407850
EM: Round [784] log likelihood: -9987.407637
EM: Round [785] log likelihood: -9987.407424
EM: Round [786] log likelihood: -9987.407212
EM: Round [787] log likelihood: -9987.407000
EM: Round [788] log likelihood: -9987.406789
EM: Round [789] log likelihood: -9987.406578
EM: Round [790] log likelihood: -9987.406368
EM: Round [791] log likelihood: -9987.406159
EM: Round [792] log likelihood: -9987.405949
EM: Round [793] log likelihood: -9987.405741
EM: Round [794] log likelihood: -9987.405533
EM: Round [795] log likelihood: -9987.405325
EM: Round [796] log likelihood: -9987.405118
EM: Round [797] log likelihood: -9987.404911
EM: Round [798] log likelihood: -9987.404705
EM: Round [799] log likelihood: -9987.404500
EM: Round [800] log likelihood: -9987.404295
EM: Round [801] log likelihood: -9987.404090
EM: Round [802] log likelihood: -9987.403886
EM: Round [803] log likelihood: -9987.403682
EM: Round [804] log likelihood: -9987.403479
EM: Round [805] log likelihood: -9987.403277
EM: Round [806] log likelihood: -9987.403074
EM: Round [807] log likelihood: -9987.402873
EM: Round [808] log likelihood: -9987.402672
EM: Round [809] log likelihood: -9987.402471
EM: Round [810] log likelihood: -9987.402271
EM: Round [811] log likelihood: -9987.402071
EM: Round [812] log likelihood: -9987.401872
EM: Round [813] log likelihood: -9987.401673
EM: Round [814] log likelihood: -9987.401475
EM: Round [815] log likelihood: -9987.401277
EM: Round [816] log likelihood: -9987.401080
EM: Round [817] log likelihood: -9987.400883
EM: Round [818] log likelihood: -9987.400687
EM: Round [819] log likelihood: -9987.400491
EM: Round [820] log likelihood: -9987.400295
EM: Round [821] log likelihood: -9987.400100
EM: Round [822] log likelihood: -9987.399906
EM: Round [823] log likelihood: -9987.399712
EM: Round [824] log likelihood: -9987.399518
EM: Round [825] log likelihood: -9987.399325
EM: Round [826] log likelihood: -9987.399133
EM: Round [827] log likelihood: -9987.398941
EM: Round [828] log likelihood: -9987.398749
EM: Round [829] log likelihood: -9987.398558
EM: Round [830] log likelihood: -9987.398367
EM: Round [831] log likelihood: -9987.398177
EM: Round [832] log likelihood: -9987.397987
EM: Round [833] log likelihood: -9987.397798
EM: Round [834] log likelihood: -9987.397609
EM: Round [835] log likelihood: -9987.397420
EM: Round [836] log likelihood: -9987.397232
EM: Round [837] log likelihood: -9987.397045
EM: Round [838] log likelihood: -9987.396858
EM: Round [839] log likelihood: -9987.396671
EM: Round [840] log likelihood: -9987.396485
EM: Round [841] log likelihood: -9987.396299
EM: Round [842] log likelihood: -9987.396114
EM: Round [843] log likelihood: -9987.395929
EM: Round [844] log likelihood: -9987.395744
EM: Round [845] log likelihood: -9987.395560
EM: Round [846] log likelihood: -9987.395377
EM: Round [847] log likelihood: -9987.395194
EM: Round [848] log likelihood: -9987.395011
EM: Round [849] log likelihood: -9987.394829
EM: Round [850] log likelihood: -9987.394647
EM: Round [851] log likelihood: -9987.394466
EM: Round [852] log likelihood: -9987.394285
EM: Round [853] log likelihood: -9987.394104
EM: Round [854] log likelihood: -9987.393924
EM: Round [855] log likelihood: -9987.393745
EM: Round [856] log likelihood: -9987.393565
EM: Round [857] log likelihood: -9987.393387
EM: Round [858] log likelihood: -9987.393208
EM: Round [859] log likelihood: -9987.393030
EM: Round [860] log likelihood: -9987.392853
EM: Round [861] log likelihood: -9987.392676
EM: Round [862] log likelihood: -9987.392499
EM: Round [863] log likelihood: -9987.392323
EM: Round [864] log likelihood: -9987.392147
EM: Round [865] log likelihood: -9987.391972
EM: Round [866] log likelihood: -9987.391797
EM: Round [867] log likelihood: -9987.391623
EM: Round [868] log likelihood: -9987.391448
EM: Round [869] log likelihood: -9987.391275
EM: Round [870] log likelihood: -9987.391101
EM: Round [871] log likelihood: -9987.390929
EM: Round [872] log likelihood: -9987.390756
EM: Round [873] log likelihood: -9987.390584
EM: Round [874] log likelihood: -9987.390412
EM: Round [875] log likelihood: -9987.390241
EM: Round [876] log likelihood: -9987.390070
EM: Round [877] log likelihood: -9987.389900
EM: Round [878] log likelihood: -9987.389730
EM: Round [879] log likelihood: -9987.389561
EM: Round [880] log likelihood: -9987.389391
EM: Round [881] log likelihood: -9987.389223
EM: Round [882] log likelihood: -9987.389054
EM: Round [883] log likelihood: -9987.388886
EM: Round [884] log likelihood: -9987.388719
EM: Round [885] log likelihood: -9987.388551
EM: Round [886] log likelihood: -9987.388385
EM: Round [887] log likelihood: -9987.388218
EM: Round [888] log likelihood: -9987.388052
EM: Round [889] log likelihood: -9987.387887
EM: Round [890] log likelihood: -9987.387722
EM: Round [891] log likelihood: -9987.387557
EM: Round [892] log likelihood: -9987.387392
EM: Round [893] log likelihood: -9987.387228
EM: Round [894] log likelihood: -9987.387065
EM: Round [895] log likelihood: -9987.386901
EM: Round [896] log likelihood: -9987.386739
EM: Round [897] log likelihood: -9987.386576
EM: Round [898] log likelihood: -9987.386414
EM: Round [899] log likelihood: -9987.386252
EM: Round [900] log likelihood: -9987.386091
EM: Round [901] log likelihood: -9987.385930
EM: Round [902] log likelihood: -9987.385770
EM: Round [903] log likelihood: -9987.385610
EM: Round [904] log likelihood: -9987.385450
EM: Round [905] log likelihood: -9987.385290
EM: Round [906] log likelihood: -9987.385131
EM: Round [907] log likelihood: -9987.384973
EM: Round [908] log likelihood: -9987.384814
EM: Round [909] log likelihood: -9987.384657
EM: Round [910] log likelihood: -9987.384499
EM: Round [911] log likelihood: -9987.384342
EM: Round [912] log likelihood: -9987.384185
EM: Round [913] log likelihood: -9987.384029
EM: Round [914] log likelihood: -9987.383873
EM: Round [915] log likelihood: -9987.383717
EM: Round [916] log likelihood: -9987.383562
EM: Round [917] log likelihood: -9987.383407
EM: Round [918] log likelihood: -9987.383252
EM: Round [919] log likelihood: -9987.383098
EM: Round [920] log likelihood: -9987.382944
EM: Round [921] log likelihood: -9987.382791
EM: Round [922] log likelihood: -9987.382638
EM: Round [923] log likelihood: -9987.382485
EM: Round [924] log likelihood: -9987.382333
EM: Round [925] log likelihood: -9987.382181
EM: Round [926] log likelihood: -9987.382029
EM: Round [927] log likelihood: -9987.381878
EM: Round [928] log likelihood: -9987.381727
EM: Round [929] log likelihood: -9987.381576
EM: Round [930] log likelihood: -9987.381426
EM: Round [931] log likelihood: -9987.381276
EM: Round [932] log likelihood: -9987.381127
EM: Round [933] log likelihood: -9987.380978
EM: Round [934] log likelihood: -9987.380829
EM: Round [935] log likelihood: -9987.380681
EM: Round [936] log likelihood: -9987.380532
EM: Round [937] log likelihood: -9987.380385
EM: Round [938] log likelihood: -9987.380237
EM: Round [939] log likelihood: -9987.380090
EM: Round [940] log likelihood: -9987.379944
EM: Round [941] log likelihood: -9987.379797
EM: Round [942] log likelihood: -9987.379651
EM: Round [943] log likelihood: -9987.379506
EM: Round [944] log likelihood: -9987.379360
EM: Round [945] log likelihood: -9987.379215
EM: Round [946] log likelihood: -9987.379071
EM: Round [947] log likelihood: -9987.378926
EM: Round [948] log likelihood: -9987.378782
EM: Round [949] log likelihood: -9987.378639
EM: Round [950] log likelihood: -9987.378496
EM: Round [951] log likelihood: -9987.378353
EM: Round [952] log likelihood: -9987.378210
EM: Round [953] log likelihood: -9987.378068
EM: Round [954] log likelihood: -9987.377926
EM: Round [955] log likelihood: -9987.377784
EM: Round [956] log likelihood: -9987.377643
EM: Round [957] log likelihood: -9987.377502
EM: Round [958] log likelihood: -9987.377362
EM: Round [959] log likelihood: -9987.377221
EM: Round [960] log likelihood: -9987.377081
EM: Round [961] log likelihood: -9987.376942
EM: Round [962] log likelihood: -9987.376803
EM: Round [963] log likelihood: -9987.376664
EM: Round [964] log likelihood: -9987.376525
EM: Round [965] log likelihood: -9987.376387
EM: Round [966] log likelihood: -9987.376249
EM: Round [967] log likelihood: -9987.376111
EM: Round [968] log likelihood: -9987.375974
EM: Round [969] log likelihood: -9987.375837
EM: Round [970] log likelihood: -9987.375700
EM: Round [971] log likelihood: -9987.375564
EM: Round [972] log likelihood: -9987.375428
EM: Round [973] log likelihood: -9987.375292
EM: Round [974] log likelihood: -9987.375157
EM: Round [975] log likelihood: -9987.375022
EM: Round [976] log likelihood: -9987.374887
EM: Round [977] log likelihood: -9987.374753
EM: Round [978] log likelihood: -9987.374619
EM: Round [979] log likelihood: -9987.374485
EM: Round [980] log likelihood: -9987.374351
EM: Round [981] log likelihood: -9987.374218
EM: Round [982] log likelihood: -9987.374085
EM: Round [983] log likelihood: -9987.373953
EM: Round [984] log likelihood: -9987.373821
EM: Round [985] log likelihood: -9987.373689
EM: Round [986] log likelihood: -9987.373557
EM: Round [987] log likelihood: -9987.373426
EM: Round [988] log likelihood: -9987.373295
EM: Round [989] log likelihood: -9987.373164
EM: Round [990] log likelihood: -9987.373034
EM: Round [991] log likelihood: -9987.372904
EM: Round [992] log likelihood: -9987.372774
EM: Round [993] log likelihood: -9987.372644
EM: Round [994] log likelihood: -9987.372515
EM: Round [995] log likelihood: -9987.372386
EM: Round [996] log likelihood: -9987.372258
EM: Round [997] log likelihood: -9987.372130
EM: Round [998] log likelihood: -9987.372002
EM: Round [999] log likelihood: -9987.371874
EM: Round [1000] log likelihood: -9987.371747
EM: Round [1001] log likelihood: -9987.371620
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz: 294805893
Execution Time = 5.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.7E4AVD1Zcz --json_outfile /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.7E4AVD1Zcz --json_outfile /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2
Running: touch /tmp/nxf.7E4AVD1Zcz/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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2 --html_output /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.04 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2 --html_output /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000270816.6]
WARNING, no entry stored in dbm for [ENSG00000270816.6]
WARNING, no entry stored in dbm for [ENSG00000270816.6]
WARNING, no entry stored in dbm for [ENSG00000227932.2]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory