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/2c/486144bd99506246abb167c835809f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/486144bd99506246abb167c835809f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/2ae7c156ed17921c996b3230b8d9b0/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/2ae7c156ed17921c996b3230b8d9b0/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/31989bd74734f6834cd6fa31a4afd4/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-";
Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+";
Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-";
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_3.fusionreport.tsv --gtf /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/cytoBand.txt
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed
-parsing GTF file: /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.tabix.ok
Running: samtools faidx /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.oDa2yAvfMx/fi_workdir --reads "/tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:15:25 ..... started STAR run
Jun 08 10:15:25 ..... loading genome
Jun 08 10:17:18 ... generating Suffix Array index
Jun 08 10:21:11 ... completed Suffix Array index
Jun 08 10:21:11 ..... processing annotations GTF
Jun 08 10:21:11 ..... inserting junctions into the genome indices
Jun 08 10:22:13 ..... started mapping
Jun 08 11:24:40 ..... finished mapping
Jun 08 11:24:42 ..... started sorting BAM
Jun 08 11:24:44 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
* Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
Execution Time = 69.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.oDa2yAvfMx/fi_workdir --reads "/tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
11:25:16 : INFO : Done.
Execution Time = 0.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
-parsing /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
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[4820000] -done parsing /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 134,
'excessive soft clipping' => 32806,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 31,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 43,
' ** passed ** ' => 35312,
'num genes matched < 2' => 21,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 60,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 55,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1422,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
'seq-similar region overlap' => 1104,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 685,
'exons hit < 2' => 11,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 32,
'per_id < 96' => 26728,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72,
'small anchor length' => 119,
'low complexity anchor region' => 26,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 308,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 212,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1111
};
-writing fusion junction support info.
Execution Time = 3.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[116000] -fusion SPANNING read extraction for scaff: AC096555.1--PCSK2
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[877000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
-fusion SPANNING read extraction for scaff: FRG1DP--MLLT10P1
-fusion SPANNING read extraction for scaff: FRG1DP--5_8S_rRNA
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[93000] -fusion SPANNING read extraction for scaff: IGH-@-ext--SPG7
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[93000] -fusion SPANNING read extraction for scaff: IGH@-ext--SPG7
[1000] -fusion SPANNING read extraction for scaff: ITGA9--AC108752.1
[1000] -fusion SPANNING read extraction for scaff: ITGA9--MRPS17P3
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[1155000] -fusion SPANNING read extraction for scaff: NPM1--MT-RNR2
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[4000] -fusion SPANNING read extraction for scaff: OR4A11P--OR4A16
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[83000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[96000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
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[98000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
[1000]
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[120000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
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[107000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
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[123000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[113000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[111000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[98000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[1000]
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[78000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10
[1000]
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[34000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
[1000]
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
[1000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
[1000]
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
[1000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
[1000]
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[58000] -fusion SPANNING read extraction for scaff: SPG7--PLSCR5
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[58000] -fusion SPANNING read extraction for scaff: SPG7--AC092957.1
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[16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL158828.1
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[16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL353613.1
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[77000] -fusion SPANNING read extraction for scaff: SUPT20H--CHRDL2
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[35000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[44000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG
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[140000] -fusion SPANNING read extraction for scaff: ZNF875--PCSK2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 213784,
'lacks exon overlap' => 72048
};
Execution Time = 8.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -16152.747457
EM: Round [1] log likelihood: -16139.164232
EM: Round [2] log likelihood: -16135.933948
EM: Round [3] log likelihood: -16133.557758
EM: Round [4] log likelihood: -16131.561569
EM: Round [5] log likelihood: -16129.836822
EM: Round [6] log likelihood: -16128.330842
EM: Round [7] log likelihood: -16127.007231
EM: Round [8] log likelihood: -16125.837873
EM: Round [9] log likelihood: -16124.800110
EM: Round [10] log likelihood: -16123.875299
EM: Round [11] log likelihood: -16123.047911
EM: Round [12] log likelihood: -16122.304895
EM: Round [13] log likelihood: -16121.635213
EM: Round [14] log likelihood: -16121.029480
EM: Round [15] log likelihood: -16120.479677
EM: Round [16] log likelihood: -16119.978928
EM: Round [17] log likelihood: -16119.521313
EM: Round [18] log likelihood: -16119.101724
EM: Round [19] log likelihood: -16118.715738
EM: Round [20] log likelihood: -16118.359516
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EM: Round [940] log likelihood: -16107.131764
EM: Round [941] log likelihood: -16107.131538
EM: Round [942] log likelihood: -16107.131314
EM: Round [943] log likelihood: -16107.131090
EM: Round [944] log likelihood: -16107.130867
EM: Round [945] log likelihood: -16107.130645
EM: Round [946] log likelihood: -16107.130423
EM: Round [947] log likelihood: -16107.130202
EM: Round [948] log likelihood: -16107.129983
EM: Round [949] log likelihood: -16107.129763
EM: Round [950] log likelihood: -16107.129545
EM: Round [951] log likelihood: -16107.129327
EM: Round [952] log likelihood: -16107.129111
EM: Round [953] log likelihood: -16107.128894
EM: Round [954] log likelihood: -16107.128679
EM: Round [955] log likelihood: -16107.128464
EM: Round [956] log likelihood: -16107.128251
EM: Round [957] log likelihood: -16107.128037
EM: Round [958] log likelihood: -16107.127825
EM: Round [959] log likelihood: -16107.127613
EM: Round [960] log likelihood: -16107.127402
EM: Round [961] log likelihood: -16107.127192
EM: Round [962] log likelihood: -16107.126983
EM: Round [963] log likelihood: -16107.126774
EM: Round [964] log likelihood: -16107.126566
EM: Round [965] log likelihood: -16107.126359
EM: Round [966] log likelihood: -16107.126152
EM: Round [967] log likelihood: -16107.125946
EM: Round [968] log likelihood: -16107.125741
EM: Round [969] log likelihood: -16107.125536
EM: Round [970] log likelihood: -16107.125333
EM: Round [971] log likelihood: -16107.125129
EM: Round [972] log likelihood: -16107.124927
EM: Round [973] log likelihood: -16107.124725
EM: Round [974] log likelihood: -16107.124524
EM: Round [975] log likelihood: -16107.124324
EM: Round [976] log likelihood: -16107.124124
EM: Round [977] log likelihood: -16107.123925
EM: Round [978] log likelihood: -16107.123727
EM: Round [979] log likelihood: -16107.123529
EM: Round [980] log likelihood: -16107.123332
EM: Round [981] log likelihood: -16107.123136
EM: Round [982] log likelihood: -16107.122940
EM: Round [983] log likelihood: -16107.122745
EM: Round [984] log likelihood: -16107.122551
EM: Round [985] log likelihood: -16107.122357
EM: Round [986] log likelihood: -16107.122164
EM: Round [987] log likelihood: -16107.121971
EM: Round [988] log likelihood: -16107.121780
EM: Round [989] log likelihood: -16107.121589
EM: Round [990] log likelihood: -16107.121398
EM: Round [991] log likelihood: -16107.121208
EM: Round [992] log likelihood: -16107.121019
EM: Round [993] log likelihood: -16107.120830
EM: Round [994] log likelihood: -16107.120642
EM: Round [995] log likelihood: -16107.120455
EM: Round [996] log likelihood: -16107.120268
EM: Round [997] log likelihood: -16107.120082
EM: Round [998] log likelihood: -16107.119897
EM: Round [999] log likelihood: -16107.119712
EM: Round [1000] log likelihood: -16107.119528
EM: Round [1001] log likelihood: -16107.119344
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam"
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || :
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords
CMD: touch /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir
-done, see /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7498.098323
EM: Round [1] log likelihood: -7496.217878
EM: Round [2] log likelihood: -7496.217867
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 295197448
Execution Time = 5.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/fi_workdir/microH.dat
Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.oDa2yAvfMx/fi_workdir/microH.dat
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.oDa2yAvfMx/fi_workdir/microH.dat /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.oDa2yAvfMx/fi_workdir/microH.dat /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oDa2yAvfMx --json_outfile /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oDa2yAvfMx --json_outfile /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3
Running: touch /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.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 [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000286152.1]
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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oDa2yAvfMx/ctat_genome_lib_build_dir > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.oDa2yAvfMx/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory