Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/ae5d6267e7065a01cce832eb574c1f/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/648b4e693e602dff96cf0912bd7988/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/648b4e693e602dff96cf0912bd7988/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/ae5d6267e7065a01cce832eb574c1f/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/726bc5417bdc9c71ff6375aaf22826/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/cytoBand.txt
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.Nedor2At7D/fi_workdir --reads "/tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Nedor2At7D/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.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:17:39 ..... started STAR run
Jun 08 10:17:39 ..... loading genome
Jun 08 10:19:33 ... generating Suffix Array index
Jun 08 10:24:22 ... completed Suffix Array index
Jun 08 10:24:22 ..... processing annotations GTF
Jun 08 10:24:22 ..... inserting junctions into the genome indices
Jun 08 10:25:35 ..... started mapping
Jun 08 11:46:06 ..... finished mapping
Jun 08 11:46:09 ..... started sorting BAM
Jun 08 11:46:09 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 88.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.Nedor2At7D/fi_workdir --reads "/tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:46:20 : INFO : Done.
Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[1610000] -done parsing /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
'seq-similar region overlap' => 129,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 23,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
'excessive soft clipping' => 9073,
'low complexity anchor region' => 11,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 116,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num genes matched < 2' => 16,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'per_id < 96' => 6308,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
'small anchor length' => 101,
' ** passed ** ' => 18595
};
-writing fusion junction support info.
Execution Time = 0.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[175000] -fusion SPANNING read extraction for scaff: CCDC6--RET
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[28000] -fusion SPANNING read extraction for scaff: DENND5B--AC087311.1
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[28000] -fusion SPANNING read extraction for scaff: DENND5B--SYT10
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[25000] -fusion SPANNING read extraction for scaff: DNAJC1--SPAG6
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[20000] -fusion SPANNING read extraction for scaff: DNAJC1--AL513128.1
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[79000] -fusion SPANNING read extraction for scaff: EIF2S3--KLHL15
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[41000] -fusion SPANNING read extraction for scaff: EIF3H--SLC30A8
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[18000] -fusion SPANNING read extraction for scaff: MIPEP--CYCSP33
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[18000] -fusion SPANNING read extraction for scaff: MIPEP--TPTE2P6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[60000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[60000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[61000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[242000] -fusion SPANNING read extraction for scaff: RAI1--MYO15A
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[90000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[33000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[25000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[33000] -fusion SPANNING read extraction for scaff: VPS8--AC099560.1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 56503,
'lacks exon overlap' => 4692
};
Execution Time = 2.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -8183.687660
EM: Round [1] log likelihood: -8172.621639
EM: Round [2] log likelihood: -8171.805988
EM: Round [3] log likelihood: -8171.121769
EM: Round [4] log likelihood: -8170.526110
EM: Round [5] log likelihood: -8170.004186
EM: Round [6] log likelihood: -8169.544449
EM: Round [7] log likelihood: -8169.137402
EM: Round [8] log likelihood: -8168.775177
EM: Round [9] log likelihood: -8168.451220
EM: Round [10] log likelihood: -8168.160055
EM: Round [11] log likelihood: -8167.897088
EM: Round [12] log likelihood: -8167.658452
EM: Round [13] log likelihood: -8167.440884
EM: Round [14] log likelihood: -8167.241621
EM: Round [15] log likelihood: -8167.058320
EM: Round [16] log likelihood: -8166.888985
EM: Round [17] log likelihood: -8166.731916
EM: Round [18] log likelihood: -8166.585661
EM: Round [19] log likelihood: -8166.448974
EM: Round [20] log likelihood: -8166.320785
EM: Round [21] log likelihood: -8166.200173
EM: Round [22] log likelihood: -8166.086344
EM: Round [23] log likelihood: -8165.978611
EM: Round [24] log likelihood: -8165.876377
EM: Round [25] log likelihood: -8165.779123
EM: Round [26] log likelihood: -8165.686397
EM: Round [27] log likelihood: -8165.597801
EM: Round [28] log likelihood: -8165.512990
EM: Round [29] log likelihood: -8165.431656
EM: Round [30] log likelihood: -8165.353530
EM: Round [31] log likelihood: -8165.278371
EM: Round [32] log likelihood: -8165.205967
EM: Round [33] log likelihood: -8165.136128
EM: Round [34] log likelihood: -8165.068683
EM: Round [35] log likelihood: -8165.003480
EM: Round [36] log likelihood: -8164.940380
EM: Round [37] log likelihood: -8164.879259
EM: Round [38] log likelihood: -8164.820004
EM: Round [39] log likelihood: -8164.762512
EM: Round [40] log likelihood: -8164.706687
EM: Round [41] log likelihood: -8164.652444
EM: Round [42] log likelihood: -8164.599703
EM: Round [43] log likelihood: -8164.548391
EM: Round [44] log likelihood: -8164.498440
EM: Round [45] log likelihood: -8164.449786
EM: Round [46] log likelihood: -8164.402372
EM: Round [47] log likelihood: -8164.356143
EM: Round [48] log likelihood: -8164.311047
EM: Round [49] log likelihood: -8164.267037
EM: Round [50] log likelihood: -8164.224069
EM: Round [51] log likelihood: -8164.182099
EM: Round [52] log likelihood: -8164.141090
EM: Round [53] log likelihood: -8164.101002
EM: Round [54] log likelihood: -8164.061801
EM: Round [55] log likelihood: -8164.023453
EM: Round [56] log likelihood: -8163.985928
EM: Round [57] log likelihood: -8163.949194
EM: Round [58] log likelihood: -8163.913223
EM: Round [59] log likelihood: -8163.877989
EM: Round [60] log likelihood: -8163.843466
EM: Round [61] log likelihood: -8163.809629
EM: Round [62] log likelihood: -8163.776456
EM: Round [63] log likelihood: -8163.743923
EM: Round [64] log likelihood: -8163.712009
EM: Round [65] log likelihood: -8163.680695
EM: Round [66] log likelihood: -8163.649962
EM: Round [67] log likelihood: -8163.619790
EM: Round [68] log likelihood: -8163.590162
EM: Round [69] log likelihood: -8163.561061
EM: Round [70] log likelihood: -8163.532472
EM: Round [71] log likelihood: -8163.504378
EM: Round [72] log likelihood: -8163.476765
EM: Round [73] log likelihood: -8163.449619
EM: Round [74] log likelihood: -8163.422926
EM: Round [75] log likelihood: -8163.396673
EM: Round [76] log likelihood: -8163.370848
EM: Round [77] log likelihood: -8163.345438
EM: Round [78] log likelihood: -8163.320432
EM: Round [79] log likelihood: -8163.295819
EM: Round [80] log likelihood: -8163.271588
EM: Round [81] log likelihood: -8163.247729
EM: Round [82] log likelihood: -8163.224233
EM: Round [83] log likelihood: -8163.201089
EM: Round [84] log likelihood: -8163.178289
EM: Round [85] log likelihood: -8163.155824
EM: Round [86] log likelihood: -8163.133685
EM: Round [87] log likelihood: -8163.111864
EM: Round [88] log likelihood: -8163.090355
EM: Round [89] log likelihood: -8163.069148
EM: Round [90] log likelihood: -8163.048236
EM: Round [91] log likelihood: -8163.027614
EM: Round [92] log likelihood: -8163.007273
EM: Round [93] log likelihood: -8162.987208
EM: Round [94] log likelihood: -8162.967412
EM: Round [95] log likelihood: -8162.947879
EM: Round [96] log likelihood: -8162.928603
EM: Round [97] log likelihood: -8162.909578
EM: Round [98] log likelihood: -8162.890799
EM: Round [99] log likelihood: -8162.872261
EM: Round [100] log likelihood: -8162.853959
EM: Round [101] log likelihood: -8162.835887
EM: Round [102] log likelihood: -8162.818041
EM: Round [103] log likelihood: -8162.800416
EM: Round [104] log likelihood: -8162.783008
EM: Round [105] log likelihood: -8162.765811
EM: Round [106] log likelihood: -8162.748823
EM: Round [107] log likelihood: -8162.732039
EM: Round [108] log likelihood: -8162.715455
EM: Round [109] log likelihood: -8162.699067
EM: Round [110] log likelihood: -8162.682871
EM: Round [111] log likelihood: -8162.666864
EM: Round [112] log likelihood: -8162.651042
EM: Round [113] log likelihood: -8162.635402
EM: Round [114] log likelihood: -8162.619941
EM: Round [115] log likelihood: -8162.604654
EM: Round [116] log likelihood: -8162.589540
EM: Round [117] log likelihood: -8162.574595
EM: Round [118] log likelihood: -8162.559816
EM: Round [119] log likelihood: -8162.545201
EM: Round [120] log likelihood: -8162.530745
EM: Round [121] log likelihood: -8162.516448
EM: Round [122] log likelihood: -8162.502305
EM: Round [123] log likelihood: -8162.488315
EM: Round [124] log likelihood: -8162.474475
EM: Round [125] log likelihood: -8162.460782
EM: Round [126] log likelihood: -8162.447234
EM: Round [127] log likelihood: -8162.433829
EM: Round [128] log likelihood: -8162.420565
EM: Round [129] log likelihood: -8162.407439
EM: Round [130] log likelihood: -8162.394448
EM: Round [131] log likelihood: -8162.381592
EM: Round [132] log likelihood: -8162.368868
EM: Round [133] log likelihood: -8162.356273
EM: Round [134] log likelihood: -8162.343807
EM: Round [135] log likelihood: -8162.331466
EM: Round [136] log likelihood: -8162.319250
EM: Round [137] log likelihood: -8162.307156
EM: Round [138] log likelihood: -8162.295182
EM: Round [139] log likelihood: -8162.283327
EM: Round [140] log likelihood: -8162.271589
EM: Round [141] log likelihood: -8162.259966
EM: Round [142] log likelihood: -8162.248457
EM: Round [143] log likelihood: -8162.237060
EM: Round [144] log likelihood: -8162.225774
EM: Round [145] log likelihood: -8162.214596
EM: Round [146] log likelihood: -8162.203526
EM: Round [147] log likelihood: -8162.192562
EM: Round [148] log likelihood: -8162.181702
EM: Round [149] log likelihood: -8162.170946
EM: Round [150] log likelihood: -8162.160291
EM: Round [151] log likelihood: -8162.149737
EM: Round [152] log likelihood: -8162.139281
EM: Round [153] log likelihood: -8162.128924
EM: Round [154] log likelihood: -8162.118662
EM: Round [155] log likelihood: -8162.108496
EM: Round [156] log likelihood: -8162.098424
EM: Round [157] log likelihood: -8162.088445
EM: Round [158] log likelihood: -8162.078557
EM: Round [159] log likelihood: -8162.068760
EM: Round [160] log likelihood: -8162.059051
EM: Round [161] log likelihood: -8162.049431
EM: Round [162] log likelihood: -8162.039898
EM: Round [163] log likelihood: -8162.030451
EM: Round [164] log likelihood: -8162.021088
EM: Round [165] log likelihood: -8162.011810
EM: Round [166] log likelihood: -8162.002614
EM: Round [167] log likelihood: -8161.993500
EM: Round [168] log likelihood: -8161.984467
EM: Round [169] log likelihood: -8161.975513
EM: Round [170] log likelihood: -8161.966639
EM: Round [171] log likelihood: -8161.957842
EM: Round [172] log likelihood: -8161.949123
EM: Round [173] log likelihood: -8161.940479
EM: Round [174] log likelihood: -8161.931911
EM: Round [175] log likelihood: -8161.923416
EM: Round [176] log likelihood: -8161.914996
EM: Round [177] log likelihood: -8161.906648
EM: Round [178] log likelihood: -8161.898371
EM: Round [179] log likelihood: -8161.890166
EM: Round [180] log likelihood: -8161.882031
EM: Round [181] log likelihood: -8161.873965
EM: Round [182] log likelihood: -8161.865968
EM: Round [183] log likelihood: -8161.858038
EM: Round [184] log likelihood: -8161.850175
EM: Round [185] log likelihood: -8161.842379
EM: Round [186] log likelihood: -8161.834648
EM: Round [187] log likelihood: -8161.826982
EM: Round [188] log likelihood: -8161.819380
EM: Round [189] log likelihood: -8161.811841
EM: Round [190] log likelihood: -8161.804365
EM: Round [191] log likelihood: -8161.796951
EM: Round [192] log likelihood: -8161.789599
EM: Round [193] log likelihood: -8161.782307
EM: Round [194] log likelihood: -8161.775075
EM: Round [195] log likelihood: -8161.767902
EM: Round [196] log likelihood: -8161.760789
EM: Round [197] log likelihood: -8161.753733
EM: Round [198] log likelihood: -8161.746735
EM: Round [199] log likelihood: -8161.739793
EM: Round [200] log likelihood: -8161.732908
EM: Round [201] log likelihood: -8161.726079
EM: Round [202] log likelihood: -8161.719304
EM: Round [203] log likelihood: -8161.712585
EM: Round [204] log likelihood: -8161.705919
EM: Round [205] log likelihood: -8161.699307
EM: Round [206] log likelihood: -8161.692747
EM: Round [207] log likelihood: -8161.686240
EM: Round [208] log likelihood: -8161.679785
EM: Round [209] log likelihood: -8161.673381
EM: Round [210] log likelihood: -8161.667028
EM: Round [211] log likelihood: -8161.660725
EM: Round [212] log likelihood: -8161.654471
EM: Round [213] log likelihood: -8161.648267
EM: Round [214] log likelihood: -8161.642112
EM: Round [215] log likelihood: -8161.636005
EM: Round [216] log likelihood: -8161.629946
EM: Round [217] log likelihood: -8161.623934
EM: Round [218] log likelihood: -8161.617968
EM: Round [219] log likelihood: -8161.612050
EM: Round [220] log likelihood: -8161.606177
EM: Round [221] log likelihood: -8161.600349
EM: Round [222] log likelihood: -8161.594567
EM: Round [223] log likelihood: -8161.588829
EM: Round [224] log likelihood: -8161.583136
EM: Round [225] log likelihood: -8161.577486
EM: Round [226] log likelihood: -8161.571879
EM: Round [227] log likelihood: -8161.566315
EM: Round [228] log likelihood: -8161.560794
EM: Round [229] log likelihood: -8161.555315
EM: Round [230] log likelihood: -8161.549878
EM: Round [231] log likelihood: -8161.544482
EM: Round [232] log likelihood: -8161.539126
EM: Round [233] log likelihood: -8161.533812
EM: Round [234] log likelihood: -8161.528537
EM: Round [235] log likelihood: -8161.523302
EM: Round [236] log likelihood: -8161.518107
EM: Round [237] log likelihood: -8161.512950
EM: Round [238] log likelihood: -8161.507833
EM: Round [239] log likelihood: -8161.502753
EM: Round [240] log likelihood: -8161.497712
EM: Round [241] log likelihood: -8161.492708
EM: Round [242] log likelihood: -8161.487741
EM: Round [243] log likelihood: -8161.482811
EM: Round [244] log likelihood: -8161.477918
EM: Round [245] log likelihood: -8161.473061
EM: Round [246] log likelihood: -8161.468240
EM: Round [247] log likelihood: -8161.463455
EM: Round [248] log likelihood: -8161.458704
EM: Round [249] log likelihood: -8161.453989
EM: Round [250] log likelihood: -8161.449308
EM: Round [251] log likelihood: -8161.444662
EM: Round [252] log likelihood: -8161.440050
EM: Round [253] log likelihood: -8161.435471
EM: Round [254] log likelihood: -8161.430926
EM: Round [255] log likelihood: -8161.426414
EM: Round [256] log likelihood: -8161.421935
EM: Round [257] log likelihood: -8161.417488
EM: Round [258] log likelihood: -8161.413074
EM: Round [259] log likelihood: -8161.408691
EM: Round [260] log likelihood: -8161.404340
EM: Round [261] log likelihood: -8161.400021
EM: Round [262] log likelihood: -8161.395732
EM: Round [263] log likelihood: -8161.391475
EM: Round [264] log likelihood: -8161.387248
EM: Round [265] log likelihood: -8161.383052
EM: Round [266] log likelihood: -8161.378885
EM: Round [267] log likelihood: -8161.374749
EM: Round [268] log likelihood: -8161.370641
EM: Round [269] log likelihood: -8161.366564
EM: Round [270] log likelihood: -8161.362515
EM: Round [271] log likelihood: -8161.358495
EM: Round [272] log likelihood: -8161.354504
EM: Round [273] log likelihood: -8161.350540
EM: Round [274] log likelihood: -8161.346605
EM: Round [275] log likelihood: -8161.342698
EM: Round [276] log likelihood: -8161.338819
EM: Round [277] log likelihood: -8161.334966
EM: Round [278] log likelihood: -8161.331141
EM: Round [279] log likelihood: -8161.327343
EM: Round [280] log likelihood: -8161.323572
EM: Round [281] log likelihood: -8161.319827
EM: Round [282] log likelihood: -8161.316108
EM: Round [283] log likelihood: -8161.312415
EM: Round [284] log likelihood: -8161.308748
EM: Round [285] log likelihood: -8161.305107
EM: Round [286] log likelihood: -8161.301491
EM: Round [287] log likelihood: -8161.297900
EM: Round [288] log likelihood: -8161.294334
EM: Round [289] log likelihood: -8161.290793
EM: Round [290] log likelihood: -8161.287276
EM: Round [291] log likelihood: -8161.283784
EM: Round [292] log likelihood: -8161.280316
EM: Round [293] log likelihood: -8161.276872
EM: Round [294] log likelihood: -8161.273452
EM: Round [295] log likelihood: -8161.270055
EM: Round [296] log likelihood: -8161.266681
EM: Round [297] log likelihood: -8161.263331
EM: Round [298] log likelihood: -8161.260004
EM: Round [299] log likelihood: -8161.256700
EM: Round [300] log likelihood: -8161.253418
EM: Round [301] log likelihood: -8161.250159
EM: Round [302] log likelihood: -8161.246922
EM: Round [303] log likelihood: -8161.243707
EM: Round [304] log likelihood: -8161.240514
EM: Round [305] log likelihood: -8161.237343
EM: Round [306] log likelihood: -8161.234193
EM: Round [307] log likelihood: -8161.231065
EM: Round [308] log likelihood: -8161.227958
EM: Round [309] log likelihood: -8161.224872
EM: Round [310] log likelihood: -8161.221807
EM: Round [311] log likelihood: -8161.218762
EM: Round [312] log likelihood: -8161.215739
EM: Round [313] log likelihood: -8161.212735
EM: Round [314] log likelihood: -8161.209752
EM: Round [315] log likelihood: -8161.206789
EM: Round [316] log likelihood: -8161.203846
EM: Round [317] log likelihood: -8161.200923
EM: Round [318] log likelihood: -8161.198019
EM: Round [319] log likelihood: -8161.195135
EM: Round [320] log likelihood: -8161.192270
EM: Round [321] log likelihood: -8161.189425
EM: Round [322] log likelihood: -8161.186598
EM: Round [323] log likelihood: -8161.183790
EM: Round [324] log likelihood: -8161.181001
EM: Round [325] log likelihood: -8161.178231
EM: Round [326] log likelihood: -8161.175479
EM: Round [327] log likelihood: -8161.172745
EM: Round [328] log likelihood: -8161.170030
EM: Round [329] log likelihood: -8161.167332
EM: Round [330] log likelihood: -8161.164653
EM: Round [331] log likelihood: -8161.161991
EM: Round [332] log likelihood: -8161.159347
EM: Round [333] log likelihood: -8161.156720
EM: Round [334] log likelihood: -8161.154111
EM: Round [335] log likelihood: -8161.151519
EM: Round [336] log likelihood: -8161.148943
EM: Round [337] log likelihood: -8161.146385
EM: Round [338] log likelihood: -8161.143844
EM: Round [339] log likelihood: -8161.141320
EM: Round [340] log likelihood: -8161.138812
EM: Round [341] log likelihood: -8161.136320
EM: Round [342] log likelihood: -8161.133845
EM: Round [343] log likelihood: -8161.131386
EM: Round [344] log likelihood: -8161.128943
EM: Round [345] log likelihood: -8161.126516
EM: Round [346] log likelihood: -8161.124105
EM: Round [347] log likelihood: -8161.121710
EM: Round [348] log likelihood: -8161.119331
EM: Round [349] log likelihood: -8161.116966
EM: Round [350] log likelihood: -8161.114618
EM: Round [351] log likelihood: -8161.112284
EM: Round [352] log likelihood: -8161.109966
EM: Round [353] log likelihood: -8161.107663
EM: Round [354] log likelihood: -8161.105374
EM: Round [355] log likelihood: -8161.103101
EM: Round [356] log likelihood: -8161.100842
EM: Round [357] log likelihood: -8161.098598
EM: Round [358] log likelihood: -8161.096368
EM: Round [359] log likelihood: -8161.094153
EM: Round [360] log likelihood: -8161.091952
EM: Round [361] log likelihood: -8161.089766
EM: Round [362] log likelihood: -8161.087593
EM: Round [363] log likelihood: -8161.085434
EM: Round [364] log likelihood: -8161.083290
EM: Round [365] log likelihood: -8161.081159
EM: Round [366] log likelihood: -8161.079041
EM: Round [367] log likelihood: -8161.076938
EM: Round [368] log likelihood: -8161.074847
EM: Round [369] log likelihood: -8161.072771
EM: Round [370] log likelihood: -8161.070707
EM: Round [371] log likelihood: -8161.068657
EM: Round [372] log likelihood: -8161.066620
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EM: Round [828] log likelihood: -8160.752128
EM: Round [829] log likelihood: -8160.751986
EM: Round [830] log likelihood: -8160.751844
EM: Round [831] log likelihood: -8160.751704
EM: Round [832] log likelihood: -8160.751564
EM: Round [833] log likelihood: -8160.751425
EM: Round [834] log likelihood: -8160.751287
EM: Round [835] log likelihood: -8160.751149
EM: Round [836] log likelihood: -8160.751012
EM: Round [837] log likelihood: -8160.750876
EM: Round [838] log likelihood: -8160.750741
EM: Round [839] log likelihood: -8160.750606
EM: Round [840] log likelihood: -8160.750473
EM: Round [841] log likelihood: -8160.750340
EM: Round [842] log likelihood: -8160.750207
EM: Round [843] log likelihood: -8160.750076
EM: Round [844] log likelihood: -8160.749945
EM: Round [845] log likelihood: -8160.749815
EM: Round [846] log likelihood: -8160.749685
EM: Round [847] log likelihood: -8160.749556
EM: Round [848] log likelihood: -8160.749428
EM: Round [849] log likelihood: -8160.749301
EM: Round [850] log likelihood: -8160.749174
EM: Round [851] log likelihood: -8160.749048
EM: Round [852] log likelihood: -8160.748923
EM: Round [853] log likelihood: -8160.748799
EM: Round [854] log likelihood: -8160.748675
EM: Round [855] log likelihood: -8160.748552
EM: Round [856] log likelihood: -8160.748429
EM: Round [857] log likelihood: -8160.748307
EM: Round [858] log likelihood: -8160.748186
EM: Round [859] log likelihood: -8160.748066
EM: Round [860] log likelihood: -8160.747946
EM: Round [861] log likelihood: -8160.747827
EM: Round [862] log likelihood: -8160.747708
EM: Round [863] log likelihood: -8160.747590
EM: Round [864] log likelihood: -8160.747473
EM: Round [865] log likelihood: -8160.747356
EM: Round [866] log likelihood: -8160.747240
EM: Round [867] log likelihood: -8160.747125
EM: Round [868] log likelihood: -8160.747010
EM: Round [869] log likelihood: -8160.746896
EM: Round [870] log likelihood: -8160.746783
EM: Round [871] log likelihood: -8160.746670
EM: Round [872] log likelihood: -8160.746558
EM: Round [873] log likelihood: -8160.746446
EM: Round [874] log likelihood: -8160.746335
EM: Round [875] log likelihood: -8160.746225
EM: Round [876] log likelihood: -8160.746115
EM: Round [877] log likelihood: -8160.746006
EM: Round [878] log likelihood: -8160.745897
EM: Round [879] log likelihood: -8160.745789
EM: Round [880] log likelihood: -8160.745682
EM: Round [881] log likelihood: -8160.745575
EM: Round [882] log likelihood: -8160.745469
EM: Round [883] log likelihood: -8160.745363
EM: Round [884] log likelihood: -8160.745258
EM: Round [885] log likelihood: -8160.745154
EM: Round [886] log likelihood: -8160.745050
EM: Round [887] log likelihood: -8160.744947
EM: Round [888] log likelihood: -8160.744844
EM: Round [889] log likelihood: -8160.744742
EM: Round [890] log likelihood: -8160.744640
EM: Round [891] log likelihood: -8160.744539
EM: Round [892] log likelihood: -8160.744438
EM: Round [893] log likelihood: -8160.744338
EM: Stopping iterations at round 893 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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Nedor2At7D/fi_workdir/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7049.083718
EM: Round [1] log likelihood: -7047.029678
EM: Round [2] log likelihood: -7046.977706
EM: Round [3] log likelihood: -7046.976081
EM: Round [4] log likelihood: -7046.976032
EM: Stopping iterations at round 4 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.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295183951
Execution Time = 5.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.Nedor2At7D/fi_workdir/microH.dat
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Nedor2At7D/fi_workdir/microH.dat /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Nedor2At7D/fi_workdir/microH.dat /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Nedor2At7D --json_outfile /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Nedor2At7D --json_outfile /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.Nedor2At7D/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.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 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.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_ciJ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000231873.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Nedor2At7D/ctat_genome_lib_build_dir > /tmp/nxf.Nedor2At7D/659_ciJ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.Nedor2At7D/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory