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/e2/e007397c5e651dca3b1cbee6499b3e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/e007397c5e651dca3b1cbee6499b3e/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/46db04144dd3ab9fbbe91043c05b61/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/46db04144dd3ab9fbbe91043c05b61/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/d6cd878616aaa848bb8f90b152acdd/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.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed
-parsing GTF file: /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.tabix.ok
Running: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
May 28 22:35:49 ..... started STAR run
May 28 22:35:49 ..... loading genome
May 28 22:37:42 ... generating Suffix Array index
May 28 22:41:37 ... completed Suffix Array index
May 28 22:41:37 ..... processing annotations GTF
May 28 22:41:38 ..... inserting junctions into the genome indices
May 28 22:42:39 ..... started mapping
May 28 23:43:37 ..... finished mapping
May 28 23:43:39 ..... started sorting BAM
May 28 23:43:41 ..... 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 = 67.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
23:44:05 : INFO : Done.
Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
-parsing /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
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[3670000] -done parsing /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 43,
'seq-similar region overlap' => 1104,
'excessive soft clipping' => 24453,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 60,
'per_id < 96' => 20480,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 55,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1422,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
'num genes matched < 2' => 21,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 885,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 308,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 26,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 11,
' ** passed ** ' => 35059,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 134,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24,
'small anchor length' => 119,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
'low complexity anchor region' => 21,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 212,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 685,
'exons hit < 2' => 9
};
-writing fusion junction support info.
Execution Time = 2.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.KXy1ipFxeT/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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[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
[1000]
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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
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[98000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[120000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[107000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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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
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[78000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10
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[34000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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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
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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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' => 15034
};
Execution Time = 5.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -15045.334989
EM: Round [1] log likelihood: -15031.751764
EM: Round [2] log likelihood: -15028.521480
EM: Round [3] log likelihood: -15026.145290
EM: Round [4] log likelihood: -15024.149101
EM: Round [5] log likelihood: -15022.424354
EM: Round [6] log likelihood: -15020.918374
EM: Round [7] log likelihood: -15019.594763
EM: Round [8] log likelihood: -15018.425405
EM: Round [9] log likelihood: -15017.387642
EM: Round [10] log likelihood: -15016.462831
EM: Round [11] log likelihood: -15015.635443
EM: Round [12] log likelihood: -15014.892427
EM: Round [13] log likelihood: -15014.222745
EM: Round [14] log likelihood: -15013.617012
EM: Round [15] log likelihood: -15013.067209
EM: Round [16] log likelihood: -15012.566460
EM: Round [17] log likelihood: -15012.108845
EM: Round [18] log likelihood: -15011.689256
EM: Round [19] log likelihood: -15011.303270
EM: Round [20] log likelihood: -15010.947048
EM: Round [21] log likelihood: -15010.617253
EM: Round [22] log likelihood: -15010.310976
EM: Round [23] log likelihood: -15010.025678
EM: Round [24] log likelihood: -15009.759137
EM: Round [25] log likelihood: -15009.509408
EM: Round [26] log likelihood: -15009.274785
EM: Round [27] log likelihood: -15009.053769
EM: Round [28] log likelihood: -15008.845041
EM: Round [29] log likelihood: -15008.647438
EM: Round [30] log likelihood: -15008.459936
EM: Round [31] log likelihood: -15008.281629
EM: Round [32] log likelihood: -15008.111715
EM: Round [33] log likelihood: -15007.949484
EM: Round [34] log likelihood: -15007.794307
EM: Round [35] log likelihood: -15007.645623
EM: Round [36] log likelihood: -15007.502933
EM: Round [37] log likelihood: -15007.365792
EM: Round [38] log likelihood: -15007.233803
EM: Round [39] log likelihood: -15007.106610
EM: Round [40] log likelihood: -15006.983892
EM: Round [41] log likelihood: -15006.865362
EM: Round [42] log likelihood: -15006.750762
EM: Round [43] log likelihood: -15006.639856
EM: Round [44] log likelihood: -15006.532433
EM: Round [45] log likelihood: -15006.428300
EM: Round [46] log likelihood: -15006.327280
EM: Round [47] log likelihood: -15006.229215
EM: Round [48] log likelihood: -15006.133956
EM: Round [49] log likelihood: -15006.041369
EM: Round [50] log likelihood: -15005.951329
EM: Round [51] log likelihood: -15005.863722
EM: Round [52] log likelihood: -15005.778442
EM: Round [53] log likelihood: -15005.695388
EM: Round [54] log likelihood: -15005.614470
EM: Round [55] log likelihood: -15005.535601
EM: Round [56] log likelihood: -15005.458700
EM: Round [57] log likelihood: -15005.383693
EM: Round [58] log likelihood: -15005.310507
EM: Round [59] log likelihood: -15005.239076
EM: Round [60] log likelihood: -15005.169335
EM: Round [61] log likelihood: -15005.101226
EM: Round [62] log likelihood: -15005.034691
EM: Round [63] log likelihood: -15004.969675
EM: Round [64] log likelihood: -15004.906127
EM: Round [65] log likelihood: -15004.843999
EM: Round [66] log likelihood: -15004.783241
EM: Round [67] log likelihood: -15004.723811
EM: Round [68] log likelihood: -15004.665664
EM: Round [69] log likelihood: -15004.608760
EM: Round [70] log likelihood: -15004.553059
EM: Round [71] log likelihood: -15004.498522
EM: Round [72] log likelihood: -15004.445114
EM: Round [73] log likelihood: -15004.392800
EM: Round [74] log likelihood: -15004.341544
EM: Round [75] log likelihood: -15004.291316
EM: Round [76] log likelihood: -15004.242084
EM: Round [77] log likelihood: -15004.193818
EM: Round [78] log likelihood: -15004.146488
EM: Round [79] log likelihood: -15004.100067
EM: Round [80] log likelihood: -15004.054528
EM: Round [81] log likelihood: -15004.009844
EM: Round [82] log likelihood: -15003.965991
EM: Round [83] log likelihood: -15003.922945
EM: Round [84] log likelihood: -15003.880681
EM: Round [85] log likelihood: -15003.839177
EM: Round [86] log likelihood: -15003.798413
EM: Round [87] log likelihood: -15003.758365
EM: Round [88] log likelihood: -15003.719015
EM: Round [89] log likelihood: -15003.680343
EM: Round [90] log likelihood: -15003.642329
EM: Round [91] log likelihood: -15003.604956
EM: Round [92] log likelihood: -15003.568205
EM: Round [93] log likelihood: -15003.532060
EM: Round [94] log likelihood: -15003.496504
EM: Round [95] log likelihood: -15003.461521
EM: Round [96] log likelihood: -15003.427096
EM: Round [97] log likelihood: -15003.393214
EM: Round [98] log likelihood: -15003.359860
EM: Round [99] log likelihood: -15003.327021
EM: Round [100] log likelihood: -15003.294684
EM: Round [101] log likelihood: -15003.262834
EM: Round [102] log likelihood: -15003.231461
EM: Round [103] log likelihood: -15003.200551
EM: Round [104] log likelihood: -15003.170093
EM: Round [105] log likelihood: -15003.140076
EM: Round [106] log likelihood: -15003.110489
EM: Round [107] log likelihood: -15003.081320
EM: Round [108] log likelihood: -15003.052561
EM: Round [109] log likelihood: -15003.024201
EM: Round [110] log likelihood: -15002.996230
EM: Round [111] log likelihood: -15002.968640
EM: Round [112] log likelihood: -15002.941421
EM: Round [113] log likelihood: -15002.914564
EM: Round [114] log likelihood: -15002.888062
EM: Round [115] log likelihood: -15002.861907
EM: Round [116] log likelihood: -15002.836089
EM: Round [117] log likelihood: -15002.810603
EM: Round [118] log likelihood: -15002.785440
EM: Round [119] log likelihood: -15002.760594
EM: Round [120] log likelihood: -15002.736057
EM: Round [121] log likelihood: -15002.711823
EM: Round [122] log likelihood: -15002.687885
EM: Round [123] log likelihood: -15002.664238
EM: Round [124] log likelihood: -15002.640875
EM: Round [125] log likelihood: -15002.617790
EM: Round [126] log likelihood: -15002.594978
EM: Round [127] log likelihood: -15002.572433
EM: Round [128] log likelihood: -15002.550150
EM: Round [129] log likelihood: -15002.528123
EM: Round [130] log likelihood: -15002.506348
EM: Round [131] log likelihood: -15002.484820
EM: Round [132] log likelihood: -15002.463534
EM: Round [133] log likelihood: -15002.442485
EM: Round [134] log likelihood: -15002.421669
EM: Round [135] log likelihood: -15002.401082
EM: Round [136] log likelihood: -15002.380719
EM: Round [137] log likelihood: -15002.360577
EM: Round [138] log likelihood: -15002.340651
EM: Round [139] log likelihood: -15002.320937
EM: Round [140] log likelihood: -15002.301433
EM: Round [141] log likelihood: -15002.282133
EM: Round [142] log likelihood: -15002.263036
EM: Round [143] log likelihood: -15002.244136
EM: Round [144] log likelihood: -15002.225432
EM: Round [145] log likelihood: -15002.206919
EM: Round [146] log likelihood: -15002.188594
EM: Round [147] log likelihood: -15002.170455
EM: Round [148] log likelihood: -15002.152498
EM: Round [149] log likelihood: -15002.134721
EM: Round [150] log likelihood: -15002.117120
EM: Round [151] log likelihood: -15002.099693
EM: Round [152] log likelihood: -15002.082437
EM: Round [153] log likelihood: -15002.065350
EM: Round [154] log likelihood: -15002.048428
EM: Round [155] log likelihood: -15002.031670
EM: Round [156] log likelihood: -15002.015073
EM: Round [157] log likelihood: -15001.998634
EM: Round [158] log likelihood: -15001.982352
EM: Round [159] log likelihood: -15001.966223
EM: Round [160] log likelihood: -15001.950247
EM: Round [161] log likelihood: -15001.934419
EM: Round [162] log likelihood: -15001.918739
EM: Round [163] log likelihood: -15001.903205
EM: Round [164] log likelihood: -15001.887813
EM: Round [165] log likelihood: -15001.872563
EM: Round [166] log likelihood: -15001.857453
EM: Round [167] log likelihood: -15001.842480
EM: Round [168] log likelihood: -15001.827642
EM: Round [169] log likelihood: -15001.812939
EM: Round [170] log likelihood: -15001.798367
EM: Round [171] log likelihood: -15001.783926
EM: Round [172] log likelihood: -15001.769613
EM: Round [173] log likelihood: -15001.755427
EM: Round [174] log likelihood: -15001.741367
EM: Round [175] log likelihood: -15001.727430
EM: Round [176] log likelihood: -15001.713615
EM: Round [177] log likelihood: -15001.699921
EM: Round [178] log likelihood: -15001.686346
EM: Round [179] log likelihood: -15001.672889
EM: Round [180] log likelihood: -15001.659547
EM: Round [181] log likelihood: -15001.646321
EM: Round [182] log likelihood: -15001.633208
EM: Round [183] log likelihood: -15001.620206
EM: Round [184] log likelihood: -15001.607316
EM: Round [185] log likelihood: -15001.594534
EM: Round [186] log likelihood: -15001.581861
EM: Round [187] log likelihood: -15001.569294
EM: Round [188] log likelihood: -15001.556833
EM: Round [189] log likelihood: -15001.544476
EM: Round [190] log likelihood: -15001.532223
EM: Round [191] log likelihood: -15001.520071
EM: Round [192] log likelihood: -15001.508019
EM: Round [193] log likelihood: -15001.496068
EM: Round [194] log likelihood: -15001.484214
EM: Round [195] log likelihood: -15001.472459
EM: Round [196] log likelihood: -15001.460799
EM: Round [197] log likelihood: -15001.449234
EM: Round [198] log likelihood: -15001.437764
EM: Round [199] log likelihood: -15001.426387
EM: Round [200] log likelihood: -15001.415102
EM: Round [201] log likelihood: -15001.403908
EM: Round [202] log likelihood: -15001.392804
EM: Round [203] log likelihood: -15001.381789
EM: Round [204] log likelihood: -15001.370862
EM: Round [205] log likelihood: -15001.360022
EM: Round [206] log likelihood: -15001.349269
EM: Round [207] log likelihood: -15001.338601
EM: Round [208] log likelihood: -15001.328018
EM: Round [209] log likelihood: -15001.317518
EM: Round [210] log likelihood: -15001.307101
EM: Round [211] log likelihood: -15001.296766
EM: Round [212] log likelihood: -15001.286512
EM: Round [213] log likelihood: -15001.276338
EM: Round [214] log likelihood: -15001.266244
EM: Round [215] log likelihood: -15001.256228
EM: Round [216] log likelihood: -15001.246290
EM: Round [217] log likelihood: -15001.236428
EM: Round [218] log likelihood: -15001.226643
EM: Round [219] log likelihood: -15001.216934
EM: Round [220] log likelihood: -15001.207299
EM: Round [221] log likelihood: -15001.197738
EM: Round [222] log likelihood: -15001.188250
EM: Round [223] log likelihood: -15001.178835
EM: Round [224] log likelihood: -15001.169492
EM: Round [225] log likelihood: -15001.160220
EM: Round [226] log likelihood: -15001.151018
EM: Round [227] log likelihood: -15001.141885
EM: Round [228] log likelihood: -15001.132822
EM: Round [229] log likelihood: -15001.123827
EM: Round [230] log likelihood: -15001.114900
EM: Round [231] log likelihood: -15001.106040
EM: Round [232] log likelihood: -15001.097246
EM: Round [233] log likelihood: -15001.088518
EM: Round [234] log likelihood: -15001.079855
EM: Round [235] log likelihood: -15001.071257
EM: Round [236] log likelihood: -15001.062723
EM: Round [237] log likelihood: -15001.054252
EM: Round [238] log likelihood: -15001.045843
EM: Round [239] log likelihood: -15001.037497
EM: Round [240] log likelihood: -15001.029213
EM: Round [241] log likelihood: -15001.020989
EM: Round [242] log likelihood: -15001.012826
EM: Round [243] log likelihood: -15001.004723
EM: Round [244] log likelihood: -15000.996679
EM: Round [245] log likelihood: -15000.988694
EM: Round [246] log likelihood: -15000.980767
EM: Round [247] log likelihood: -15000.972898
EM: Round [248] log likelihood: -15000.965085
EM: Round [249] log likelihood: -15000.957330
EM: Round [250] log likelihood: -15000.949631
EM: Round [251] log likelihood: -15000.941987
EM: Round [252] log likelihood: -15000.934399
EM: Round [253] log likelihood: -15000.926865
EM: Round [254] log likelihood: -15000.919386
EM: Round [255] log likelihood: -15000.911960
EM: Round [256] log likelihood: -15000.904587
EM: Round [257] log likelihood: -15000.897267
EM: Round [258] log likelihood: -15000.889999
EM: Round [259] log likelihood: -15000.882783
EM: Round [260] log likelihood: -15000.875619
EM: Round [261] log likelihood: -15000.868505
EM: Round [262] log likelihood: -15000.861442
EM: Round [263] log likelihood: -15000.854429
EM: Round [264] log likelihood: -15000.847465
EM: Round [265] log likelihood: -15000.840551
EM: Round [266] log likelihood: -15000.833685
EM: Round [267] log likelihood: -15000.826868
EM: Round [268] log likelihood: -15000.820098
EM: Round [269] log likelihood: -15000.813376
EM: Round [270] log likelihood: -15000.806701
EM: Round [271] log likelihood: -15000.800073
EM: Round [272] log likelihood: -15000.793490
EM: Round [273] log likelihood: -15000.786954
EM: Round [274] log likelihood: -15000.780463
EM: Round [275] log likelihood: -15000.774018
EM: Round [276] log likelihood: -15000.767617
EM: Round [277] log likelihood: -15000.761260
EM: Round [278] log likelihood: -15000.754948
EM: Round [279] log likelihood: -15000.748679
EM: Round [280] log likelihood: -15000.742453
EM: Round [281] log likelihood: -15000.736270
EM: Round [282] log likelihood: -15000.730129
EM: Round [283] log likelihood: -15000.724031
EM: Round [284] log likelihood: -15000.717975
EM: Round [285] log likelihood: -15000.711960
EM: Round [286] log likelihood: -15000.705986
EM: Round [287] log likelihood: -15000.700052
EM: Round [288] log likelihood: -15000.694160
EM: Round [289] log likelihood: -15000.688307
EM: Round [290] log likelihood: -15000.682494
EM: Round [291] log likelihood: -15000.676721
EM: Round [292] log likelihood: -15000.670987
EM: Round [293] log likelihood: -15000.665291
EM: Round [294] log likelihood: -15000.659634
EM: Round [295] log likelihood: -15000.654015
EM: Round [296] log likelihood: -15000.648434
EM: Round [297] log likelihood: -15000.642891
EM: Round [298] log likelihood: -15000.637385
EM: Round [299] log likelihood: -15000.631916
EM: Round [300] log likelihood: -15000.626483
EM: Round [301] log likelihood: -15000.621087
EM: Round [302] log likelihood: -15000.615727
EM: Round [303] log likelihood: -15000.610403
EM: Round [304] log likelihood: -15000.605114
EM: Round [305] log likelihood: -15000.599860
EM: Round [306] log likelihood: -15000.594642
EM: Round [307] log likelihood: -15000.589458
EM: Round [308] log likelihood: -15000.584308
EM: Round [309] log likelihood: -15000.579192
EM: Round [310] log likelihood: -15000.574111
EM: Round [311] log likelihood: -15000.569063
EM: Round [312] log likelihood: -15000.564048
EM: Round [313] log likelihood: -15000.559066
EM: Round [314] log likelihood: -15000.554117
EM: Round [315] log likelihood: -15000.549201
EM: Round [316] log likelihood: -15000.544317
EM: Round [317] log likelihood: -15000.539465
EM: Round [318] log likelihood: -15000.534644
EM: Round [319] log likelihood: -15000.529855
EM: Round [320] log likelihood: -15000.525098
EM: Round [321] log likelihood: -15000.520371
EM: Round [322] log likelihood: -15000.515676
EM: Round [323] log likelihood: -15000.511011
EM: Round [324] log likelihood: -15000.506376
EM: Round [325] log likelihood: -15000.501771
EM: Round [326] log likelihood: -15000.497196
EM: Round [327] log likelihood: -15000.492651
EM: Round [328] log likelihood: -15000.488135
EM: Round [329] log likelihood: -15000.483649
EM: Round [330] log likelihood: -15000.479191
EM: Round [331] log likelihood: -15000.474762
EM: Round [332] log likelihood: -15000.470362
EM: Round [333] log likelihood: -15000.465990
EM: Round [334] log likelihood: -15000.461646
EM: Round [335] log likelihood: -15000.457330
EM: Round [336] log likelihood: -15000.453041
EM: Round [337] log likelihood: -15000.448780
EM: Round [338] log likelihood: -15000.444546
EM: Round [339] log likelihood: -15000.440340
EM: Round [340] log likelihood: -15000.436160
EM: Round [341] log likelihood: -15000.432006
EM: Round [342] log likelihood: -15000.427880
EM: Round [343] log likelihood: -15000.423779
EM: Round [344] log likelihood: -15000.419705
EM: Round [345] log likelihood: -15000.415656
EM: Round [346] log likelihood: -15000.411633
EM: Round [347] log likelihood: -15000.407635
EM: Round [348] log likelihood: -15000.403663
EM: Round [349] log likelihood: -15000.399716
EM: Round [350] log likelihood: -15000.395793
EM: Round [351] log likelihood: -15000.391896
EM: Round [352] log likelihood: -15000.388023
EM: Round [353] log likelihood: -15000.384174
EM: Round [354] log likelihood: -15000.380350
EM: Round [355] log likelihood: -15000.376549
EM: Round [356] log likelihood: -15000.372772
EM: Round [357] log likelihood: -15000.369019
EM: Round [358] log likelihood: -15000.365290
EM: Round [359] log likelihood: -15000.361584
EM: Round [360] log likelihood: -15000.357900
EM: Round [361] log likelihood: -15000.354240
EM: Round [362] log likelihood: -15000.350603
EM: Round [363] log likelihood: -15000.346988
EM: Round [364] log likelihood: -15000.343396
EM: Round [365] log likelihood: -15000.339826
EM: Round [366] log likelihood: -15000.336278
EM: Round [367] log likelihood: -15000.332752
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EM: Round [371] log likelihood: -15000.318865
EM: Round [372] log likelihood: -15000.315447
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EM: Round [908] log likelihood: -14999.726949
EM: Round [909] log likelihood: -14999.726696
EM: Round [910] log likelihood: -14999.726444
EM: Round [911] log likelihood: -14999.726193
EM: Round [912] log likelihood: -14999.725943
EM: Round [913] log likelihood: -14999.725694
EM: Round [914] log likelihood: -14999.725446
EM: Round [915] log likelihood: -14999.725199
EM: Round [916] log likelihood: -14999.724952
EM: Round [917] log likelihood: -14999.724707
EM: Round [918] log likelihood: -14999.724462
EM: Round [919] log likelihood: -14999.724218
EM: Round [920] log likelihood: -14999.723975
EM: Round [921] log likelihood: -14999.723733
EM: Round [922] log likelihood: -14999.723492
EM: Round [923] log likelihood: -14999.723252
EM: Round [924] log likelihood: -14999.723012
EM: Round [925] log likelihood: -14999.722774
EM: Round [926] log likelihood: -14999.722536
EM: Round [927] log likelihood: -14999.722299
EM: Round [928] log likelihood: -14999.722063
EM: Round [929] log likelihood: -14999.721828
EM: Round [930] log likelihood: -14999.721594
EM: Round [931] log likelihood: -14999.721360
EM: Round [932] log likelihood: -14999.721128
EM: Round [933] log likelihood: -14999.720896
EM: Round [934] log likelihood: -14999.720665
EM: Round [935] log likelihood: -14999.720434
EM: Round [936] log likelihood: -14999.720205
EM: Round [937] log likelihood: -14999.719977
EM: Round [938] log likelihood: -14999.719749
EM: Round [939] log likelihood: -14999.719522
EM: Round [940] log likelihood: -14999.719296
EM: Round [941] log likelihood: -14999.719070
EM: Round [942] log likelihood: -14999.718846
EM: Round [943] log likelihood: -14999.718622
EM: Round [944] log likelihood: -14999.718399
EM: Round [945] log likelihood: -14999.718177
EM: Round [946] log likelihood: -14999.717955
EM: Round [947] log likelihood: -14999.717734
EM: Round [948] log likelihood: -14999.717514
EM: Round [949] log likelihood: -14999.717295
EM: Round [950] log likelihood: -14999.717077
EM: Round [951] log likelihood: -14999.716859
EM: Round [952] log likelihood: -14999.716642
EM: Round [953] log likelihood: -14999.716426
EM: Round [954] log likelihood: -14999.716211
EM: Round [955] log likelihood: -14999.715996
EM: Round [956] log likelihood: -14999.715783
EM: Round [957] log likelihood: -14999.715569
EM: Round [958] log likelihood: -14999.715357
EM: Round [959] log likelihood: -14999.715145
EM: Round [960] log likelihood: -14999.714934
EM: Round [961] log likelihood: -14999.714724
EM: Round [962] log likelihood: -14999.714515
EM: Round [963] log likelihood: -14999.714306
EM: Round [964] log likelihood: -14999.714098
EM: Round [965] log likelihood: -14999.713891
EM: Round [966] log likelihood: -14999.713684
EM: Round [967] log likelihood: -14999.713478
EM: Round [968] log likelihood: -14999.713273
EM: Round [969] log likelihood: -14999.713068
EM: Round [970] log likelihood: -14999.712864
EM: Round [971] log likelihood: -14999.712661
EM: Round [972] log likelihood: -14999.712459
EM: Round [973] log likelihood: -14999.712257
EM: Round [974] log likelihood: -14999.712056
EM: Round [975] log likelihood: -14999.711856
EM: Round [976] log likelihood: -14999.711656
EM: Round [977] log likelihood: -14999.711457
EM: Round [978] log likelihood: -14999.711259
EM: Round [979] log likelihood: -14999.711061
EM: Round [980] log likelihood: -14999.710864
EM: Round [981] log likelihood: -14999.710668
EM: Round [982] log likelihood: -14999.710472
EM: Round [983] log likelihood: -14999.710277
EM: Round [984] log likelihood: -14999.710083
EM: Round [985] log likelihood: -14999.709889
EM: Round [986] log likelihood: -14999.709696
EM: Round [987] log likelihood: -14999.709503
EM: Round [988] log likelihood: -14999.709312
EM: Round [989] log likelihood: -14999.709121
EM: Round [990] log likelihood: -14999.708930
EM: Round [991] log likelihood: -14999.708740
EM: Round [992] log likelihood: -14999.708551
EM: Round [993] log likelihood: -14999.708362
EM: Round [994] log likelihood: -14999.708174
EM: Round [995] log likelihood: -14999.707987
EM: Round [996] log likelihood: -14999.707800
EM: Round [997] log likelihood: -14999.707614
EM: Round [998] log likelihood: -14999.707429
EM: Round [999] log likelihood: -14999.707244
EM: Round [1000] log likelihood: -14999.707060
EM: Round [1001] log likelihood: -14999.706876
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam"
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || :
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords
CMD: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/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.KXy1ipFxeT/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.KXy1ipFxeT/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.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir
-done, see /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7093.933202
EM: Round [1] log likelihood: -7092.052756
EM: Round [2] log likelihood: -7092.052745
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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 295197448
Execution Time = 5.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3
Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/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 [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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory