Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/0ca6e367151ca3d124d11c32f1d03b/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
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/77/f4889cd4b3eb61e5afc61f5c0e4a7a/659_rd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/37597b7936f7e6b3cad67b8bcf562c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/37597b7936f7e6b3cad67b8bcf562c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/f4889cd4b3eb61e5afc61f5c0e4a7a/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_rd-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_rd-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/cytoBand.txt
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.NMeURXWyeZ/fi_workdir --reads "/tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:01:59 ..... started STAR run
Jun 08 10:01:59 ..... loading genome
Jun 08 10:03:42 ... generating Suffix Array index
Jun 08 10:07:33 ... completed Suffix Array index
Jun 08 10:07:33 ..... processing annotations GTF
Jun 08 10:07:33 ..... inserting junctions into the genome indices
Jun 08 10:08:34 ..... started mapping
Jun 08 11:37:21 ..... finished mapping
Jun 08 11:37:23 ..... started sorting BAM
Jun 08 11:37:25 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 95.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.NMeURXWyeZ/fi_workdir --reads "/tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:37:47 : INFO : Done.
Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[3160000] -done parsing /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 48,
'per_id < 96' => 11571,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 48,
' ** passed ** ' => 92895,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'exons hit < 2' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 32,
'seq-similar region overlap' => 1260,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 3686,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 66,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4,
'excessive soft clipping' => 18028,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 242,
'low complexity anchor region' => 254,
'num genes matched < 2' => 521,
'small anchor length' => 404
};
-writing fusion junction support info.
Execution Time = 1.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[1201000]
[1202000] -fusion SPANNING read extraction for scaff: NAB2--STAT6
[1000]
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[3000]
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[6000]
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[8000]
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[10000]
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[32000]
[33000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[4000]
[5000]
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[10000]
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[33000]
[34000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
[1000]
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
[1000]
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
[1000]
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[6000]
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[8000]
[9000]
[10000]
[11000]
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[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
[1000]
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[33000]
[34000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
[1000]
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[4000]
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[6000]
[7000]
[8000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[80000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[73000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[33000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[1191000] -fusion SPANNING read extraction for scaff: STAT6--NAB2
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[21000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[141000] -fusion SPANNING read extraction for scaff: TMEM106B--THSD7A
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[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 37899,
'lacks exon overlap' => 88552
};
Execution Time = 4.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -26595.931124
EM: Round [1] log likelihood: -26504.739775
EM: Round [2] log likelihood: -26494.323491
EM: Round [3] log likelihood: -26485.957770
EM: Round [4] log likelihood: -26479.046297
EM: Round [5] log likelihood: -26473.287262
EM: Round [6] log likelihood: -26468.452261
EM: Round [7] log likelihood: -26464.364515
EM: Round [8] log likelihood: -26460.885438
EM: Round [9] log likelihood: -26457.905153
EM: Round [10] log likelihood: -26455.335680
EM: Round [11] log likelihood: -26453.105982
EM: Round [12] log likelihood: -26451.158306
EM: Round [13] log likelihood: -26449.445444
EM: Round [14] log likelihood: -26447.928644
EM: Round [15] log likelihood: -26446.575998
EM: Round [16] log likelihood: -26445.361163
EM: Round [17] log likelihood: -26444.262360
EM: Round [18] log likelihood: -26443.261552
EM: Round [19] log likelihood: -26442.343789
EM: Round [20] log likelihood: -26441.496665
EM: Round [21] log likelihood: -26440.709878
EM: Round [22] log likelihood: -26439.974864
EM: Round [23] log likelihood: -26439.284497
EM: Round [24] log likelihood: -26438.632839
EM: Round [25] log likelihood: -26438.014937
EM: Round [26] log likelihood: -26437.426652
EM: Round [27] log likelihood: -26436.864517
EM: Round [28] log likelihood: -26436.325623
EM: Round [29] log likelihood: -26435.807521
EM: Round [30] log likelihood: -26435.308144
EM: Round [31] log likelihood: -26434.825741
EM: Round [32] log likelihood: -26434.358823
EM: Round [33] log likelihood: -26433.906118
EM: Round [34] log likelihood: -26433.466535
EM: Round [35] log likelihood: -26433.039132
EM: Round [36] log likelihood: -26432.623091
EM: Round [37] log likelihood: -26432.217702
EM: Round [38] log likelihood: -26431.822338
EM: Round [39] log likelihood: -26431.436447
EM: Round [40] log likelihood: -26431.059539
EM: Round [41] log likelihood: -26430.691175
EM: Round [42] log likelihood: -26430.330960
EM: Round [43] log likelihood: -26429.978537
EM: Round [44] log likelihood: -26429.633579
EM: Round [45] log likelihood: -26429.295789
EM: Round [46] log likelihood: -26428.964892
EM: Round [47] log likelihood: -26428.640635
EM: Round [48] log likelihood: -26428.322781
EM: Round [49] log likelihood: -26428.011111
EM: Round [50] log likelihood: -26427.705417
EM: Round [51] log likelihood: -26427.405505
EM: Round [52] log likelihood: -26427.111193
EM: Round [53] log likelihood: -26426.822308
EM: Round [54] log likelihood: -26426.538685
EM: Round [55] log likelihood: -26426.260168
EM: Round [56] log likelihood: -26425.986610
EM: Round [57] log likelihood: -26425.717867
EM: Round [58] log likelihood: -26425.453805
EM: Round [59] log likelihood: -26425.194294
EM: Round [60] log likelihood: -26424.939210
EM: Round [61] log likelihood: -26424.688434
EM: Round [62] log likelihood: -26424.441852
EM: Round [63] log likelihood: -26424.199354
EM: Round [64] log likelihood: -26423.960835
EM: Round [65] log likelihood: -26423.726192
EM: Round [66] log likelihood: -26423.495327
EM: Round [67] log likelihood: -26423.268148
EM: Round [68] log likelihood: -26423.044562
EM: Round [69] log likelihood: -26422.824481
EM: Round [70] log likelihood: -26422.607822
EM: Round [71] log likelihood: -26422.394502
EM: Round [72] log likelihood: -26422.184443
EM: Round [73] log likelihood: -26421.977567
EM: Round [74] log likelihood: -26421.773802
EM: Round [75] log likelihood: -26421.573075
EM: Round [76] log likelihood: -26421.375318
EM: Round [77] log likelihood: -26421.180464
EM: Round [78] log likelihood: -26420.988447
EM: Round [79] log likelihood: -26420.799207
EM: Round [80] log likelihood: -26420.612680
EM: Round [81] log likelihood: -26420.428810
EM: Round [82] log likelihood: -26420.247539
EM: Round [83] log likelihood: -26420.068810
EM: Round [84] log likelihood: -26419.892572
EM: Round [85] log likelihood: -26419.718772
EM: Round [86] log likelihood: -26419.547358
EM: Round [87] log likelihood: -26419.378284
EM: Round [88] log likelihood: -26419.211499
EM: Round [89] log likelihood: -26419.046960
EM: Round [90] log likelihood: -26418.884620
EM: Round [91] log likelihood: -26418.724436
EM: Round [92] log likelihood: -26418.566365
EM: Round [93] log likelihood: -26418.410367
EM: Round [94] log likelihood: -26418.256402
EM: Round [95] log likelihood: -26418.104430
EM: Round [96] log likelihood: -26417.954413
EM: Round [97] log likelihood: -26417.806315
EM: Round [98] log likelihood: -26417.660100
EM: Round [99] log likelihood: -26417.515733
EM: Round [100] log likelihood: -26417.373179
EM: Round [101] log likelihood: -26417.232406
EM: Round [102] log likelihood: -26417.093382
EM: Round [103] log likelihood: -26416.956075
EM: Round [104] log likelihood: -26416.820454
EM: Round [105] log likelihood: -26416.686490
EM: Round [106] log likelihood: -26416.554153
EM: Round [107] log likelihood: -26416.423416
EM: Round [108] log likelihood: -26416.294249
EM: Round [109] log likelihood: -26416.166628
EM: Round [110] log likelihood: -26416.040524
EM: Round [111] log likelihood: -26415.915913
EM: Round [112] log likelihood: -26415.792769
EM: Round [113] log likelihood: -26415.671068
EM: Round [114] log likelihood: -26415.550786
EM: Round [115] log likelihood: -26415.431899
EM: Round [116] log likelihood: -26415.314385
EM: Round [117] log likelihood: -26415.198222
EM: Round [118] log likelihood: -26415.083388
EM: Round [119] log likelihood: -26414.969861
EM: Round [120] log likelihood: -26414.857621
EM: Round [121] log likelihood: -26414.746647
EM: Round [122] log likelihood: -26414.636919
EM: Round [123] log likelihood: -26414.528419
EM: Round [124] log likelihood: -26414.421126
EM: Round [125] log likelihood: -26414.315023
EM: Round [126] log likelihood: -26414.210092
EM: Round [127] log likelihood: -26414.106313
EM: Round [128] log likelihood: -26414.003671
EM: Round [129] log likelihood: -26413.902148
EM: Round [130] log likelihood: -26413.801726
EM: Round [131] log likelihood: -26413.702391
EM: Round [132] log likelihood: -26413.604126
EM: Round [133] log likelihood: -26413.506915
EM: Round [134] log likelihood: -26413.410742
EM: Round [135] log likelihood: -26413.315593
EM: Round [136] log likelihood: -26413.221454
EM: Round [137] log likelihood: -26413.128309
EM: Round [138] log likelihood: -26413.036144
EM: Round [139] log likelihood: -26412.944946
EM: Round [140] log likelihood: -26412.854700
EM: Round [141] log likelihood: -26412.765394
EM: Round [142] log likelihood: -26412.677015
EM: Round [143] log likelihood: -26412.589549
EM: Round [144] log likelihood: -26412.502984
EM: Round [145] log likelihood: -26412.417307
EM: Round [146] log likelihood: -26412.332507
EM: Round [147] log likelihood: -26412.248572
EM: Round [148] log likelihood: -26412.165489
EM: Round [149] log likelihood: -26412.083248
EM: Round [150] log likelihood: -26412.001837
EM: Round [151] log likelihood: -26411.921245
EM: Round [152] log likelihood: -26411.841462
EM: Round [153] log likelihood: -26411.762476
EM: Round [154] log likelihood: -26411.684277
EM: Round [155] log likelihood: -26411.606855
EM: Round [156] log likelihood: -26411.530199
EM: Round [157] log likelihood: -26411.454301
EM: Round [158] log likelihood: -26411.379150
EM: Round [159] log likelihood: -26411.304736
EM: Round [160] log likelihood: -26411.231050
EM: Round [161] log likelihood: -26411.158083
EM: Round [162] log likelihood: -26411.085826
EM: Round [163] log likelihood: -26411.014270
EM: Round [164] log likelihood: -26410.943406
EM: Round [165] log likelihood: -26410.873226
EM: Round [166] log likelihood: -26410.803720
EM: Round [167] log likelihood: -26410.734881
EM: Round [168] log likelihood: -26410.666700
EM: Round [169] log likelihood: -26410.599170
EM: Round [170] log likelihood: -26410.532282
EM: Round [171] log likelihood: -26410.466028
EM: Round [172] log likelihood: -26410.400402
EM: Round [173] log likelihood: -26410.335395
EM: Round [174] log likelihood: -26410.270999
EM: Round [175] log likelihood: -26410.207208
EM: Round [176] log likelihood: -26410.144015
EM: Round [177] log likelihood: -26410.081412
EM: Round [178] log likelihood: -26410.019392
EM: Round [179] log likelihood: -26409.957948
EM: Round [180] log likelihood: -26409.897074
EM: Round [181] log likelihood: -26409.836763
EM: Round [182] log likelihood: -26409.777008
EM: Round [183] log likelihood: -26409.717804
EM: Round [184] log likelihood: -26409.659143
EM: Round [185] log likelihood: -26409.601019
EM: Round [186] log likelihood: -26409.543426
EM: Round [187] log likelihood: -26409.486359
EM: Round [188] log likelihood: -26409.429810
EM: Round [189] log likelihood: -26409.373775
EM: Round [190] log likelihood: -26409.318247
EM: Round [191] log likelihood: -26409.263221
EM: Round [192] log likelihood: -26409.208691
EM: Round [193] log likelihood: -26409.154651
EM: Round [194] log likelihood: -26409.101097
EM: Round [195] log likelihood: -26409.048022
EM: Round [196] log likelihood: -26408.995421
EM: Round [197] log likelihood: -26408.943289
EM: Round [198] log likelihood: -26408.891622
EM: Round [199] log likelihood: -26408.840413
EM: Round [200] log likelihood: -26408.789658
EM: Round [201] log likelihood: -26408.739351
EM: Round [202] log likelihood: -26408.689489
EM: Round [203] log likelihood: -26408.640066
EM: Round [204] log likelihood: -26408.591077
EM: Round [205] log likelihood: -26408.542518
EM: Round [206] log likelihood: -26408.494384
EM: Round [207] log likelihood: -26408.446670
EM: Round [208] log likelihood: -26408.399373
EM: Round [209] log likelihood: -26408.352487
EM: Round [210] log likelihood: -26408.306009
EM: Round [211] log likelihood: -26408.259933
EM: Round [212] log likelihood: -26408.214257
EM: Round [213] log likelihood: -26408.168974
EM: Round [214] log likelihood: -26408.124083
EM: Round [215] log likelihood: -26408.079577
EM: Round [216] log likelihood: -26408.035454
EM: Round [217] log likelihood: -26407.991709
EM: Round [218] log likelihood: -26407.948339
EM: Round [219] log likelihood: -26407.905339
EM: Round [220] log likelihood: -26407.862706
EM: Round [221] log likelihood: -26407.820436
EM: Round [222] log likelihood: -26407.778525
EM: Round [223] log likelihood: -26407.736969
EM: Round [224] log likelihood: -26407.695766
EM: Round [225] log likelihood: -26407.654911
EM: Round [226] log likelihood: -26407.614401
EM: Round [227] log likelihood: -26407.574232
EM: Round [228] log likelihood: -26407.534401
EM: Round [229] log likelihood: -26407.494904
EM: Round [230] log likelihood: -26407.455739
EM: Round [231] log likelihood: -26407.416902
EM: Round [232] log likelihood: -26407.378389
EM: Round [233] log likelihood: -26407.340198
EM: Round [234] log likelihood: -26407.302324
EM: Round [235] log likelihood: -26407.264766
EM: Round [236] log likelihood: -26407.227520
EM: Round [237] log likelihood: -26407.190582
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EM: Round [699] log likelihood: -26402.459314
EM: Round [700] log likelihood: -26402.457905
EM: Round [701] log likelihood: -26402.456505
EM: Round [702] log likelihood: -26402.455114
EM: Round [703] log likelihood: -26402.453732
EM: Round [704] log likelihood: -26402.452358
EM: Round [705] log likelihood: -26402.450994
EM: Round [706] log likelihood: -26402.449639
EM: Round [707] log likelihood: -26402.448292
EM: Round [708] log likelihood: -26402.446954
EM: Round [709] log likelihood: -26402.445625
EM: Round [710] log likelihood: -26402.444304
EM: Round [711] log likelihood: -26402.442992
EM: Round [712] log likelihood: -26402.441688
EM: Round [713] log likelihood: -26402.440393
EM: Round [714] log likelihood: -26402.439106
EM: Round [715] log likelihood: -26402.437828
EM: Round [716] log likelihood: -26402.436557
EM: Round [717] log likelihood: -26402.435295
EM: Round [718] log likelihood: -26402.434041
EM: Round [719] log likelihood: -26402.432796
EM: Round [720] log likelihood: -26402.431558
EM: Round [721] log likelihood: -26402.430328
EM: Round [722] log likelihood: -26402.429106
EM: Round [723] log likelihood: -26402.427892
EM: Round [724] log likelihood: -26402.426686
EM: Round [725] log likelihood: -26402.425488
EM: Round [726] log likelihood: -26402.424297
EM: Round [727] log likelihood: -26402.423114
EM: Round [728] log likelihood: -26402.421939
EM: Round [729] log likelihood: -26402.420771
EM: Round [730] log likelihood: -26402.419610
EM: Round [731] log likelihood: -26402.418458
EM: Round [732] log likelihood: -26402.417312
EM: Round [733] log likelihood: -26402.416174
EM: Round [734] log likelihood: -26402.415044
EM: Round [735] log likelihood: -26402.413920
EM: Round [736] log likelihood: -26402.412804
EM: Round [737] log likelihood: -26402.411695
EM: Round [738] log likelihood: -26402.410593
EM: Round [739] log likelihood: -26402.409499
EM: Round [740] log likelihood: -26402.408411
EM: Round [741] log likelihood: -26402.407330
EM: Round [742] log likelihood: -26402.406257
EM: Round [743] log likelihood: -26402.405190
EM: Round [744] log likelihood: -26402.404130
EM: Round [745] log likelihood: -26402.403076
EM: Round [746] log likelihood: -26402.402030
EM: Round [747] log likelihood: -26402.400990
EM: Round [748] log likelihood: -26402.399957
EM: Round [749] log likelihood: -26402.398931
EM: Round [750] log likelihood: -26402.397911
EM: Round [751] log likelihood: -26402.396898
EM: Round [752] log likelihood: -26402.395891
EM: Round [753] log likelihood: -26402.394891
EM: Round [754] log likelihood: -26402.393897
EM: Round [755] log likelihood: -26402.392909
EM: Round [756] log likelihood: -26402.391928
EM: Round [757] log likelihood: -26402.390953
EM: Round [758] log likelihood: -26402.389985
EM: Round [759] log likelihood: -26402.389022
EM: Round [760] log likelihood: -26402.388066
EM: Round [761] log likelihood: -26402.387116
EM: Round [762] log likelihood: -26402.386172
EM: Round [763] log likelihood: -26402.385234
EM: Round [764] log likelihood: -26402.384302
EM: Round [765] log likelihood: -26402.383376
EM: Round [766] log likelihood: -26402.382456
EM: Round [767] log likelihood: -26402.381541
EM: Round [768] log likelihood: -26402.380633
EM: Round [769] log likelihood: -26402.379730
EM: Round [770] log likelihood: -26402.378834
EM: Round [771] log likelihood: -26402.377943
EM: Round [772] log likelihood: -26402.377057
EM: Round [773] log likelihood: -26402.376178
EM: Round [774] log likelihood: -26402.375303
EM: Round [775] log likelihood: -26402.374435
EM: Round [776] log likelihood: -26402.373572
EM: Round [777] log likelihood: -26402.372715
EM: Round [778] log likelihood: -26402.371863
EM: Round [779] log likelihood: -26402.371016
EM: Round [780] log likelihood: -26402.370175
EM: Round [781] log likelihood: -26402.369339
EM: Round [782] log likelihood: -26402.368509
EM: Round [783] log likelihood: -26402.367684
EM: Round [784] log likelihood: -26402.366864
EM: Round [785] log likelihood: -26402.366049
EM: Round [786] log likelihood: -26402.365240
EM: Round [787] log likelihood: -26402.364436
EM: Round [788] log likelihood: -26402.363636
EM: Round [789] log likelihood: -26402.362842
EM: Round [790] log likelihood: -26402.362053
EM: Round [791] log likelihood: -26402.361269
EM: Round [792] log likelihood: -26402.360490
EM: Round [793] log likelihood: -26402.359716
EM: Round [794] log likelihood: -26402.358947
EM: Round [795] log likelihood: -26402.358183
EM: Round [796] log likelihood: -26402.357424
EM: Round [797] log likelihood: -26402.356669
EM: Round [798] log likelihood: -26402.355920
EM: Round [799] log likelihood: -26402.355175
EM: Round [800] log likelihood: -26402.354435
EM: Round [801] log likelihood: -26402.353699
EM: Round [802] log likelihood: -26402.352968
EM: Round [803] log likelihood: -26402.352242
EM: Round [804] log likelihood: -26402.351521
EM: Round [805] log likelihood: -26402.350804
EM: Round [806] log likelihood: -26402.350091
EM: Round [807] log likelihood: -26402.349383
EM: Round [808] log likelihood: -26402.348680
EM: Round [809] log likelihood: -26402.347981
EM: Round [810] log likelihood: -26402.347287
EM: Round [811] log likelihood: -26402.346596
EM: Round [812] log likelihood: -26402.345911
EM: Round [813] log likelihood: -26402.345229
EM: Round [814] log likelihood: -26402.344552
EM: Round [815] log likelihood: -26402.343880
EM: Round [816] log likelihood: -26402.343211
EM: Round [817] log likelihood: -26402.342547
EM: Round [818] log likelihood: -26402.341887
EM: Round [819] log likelihood: -26402.341231
EM: Round [820] log likelihood: -26402.340580
EM: Round [821] log likelihood: -26402.339932
EM: Round [822] log likelihood: -26402.339289
EM: Round [823] log likelihood: -26402.338649
EM: Round [824] log likelihood: -26402.338014
EM: Round [825] log likelihood: -26402.337383
EM: Round [826] log likelihood: -26402.336755
EM: Round [827] log likelihood: -26402.336132
EM: Round [828] log likelihood: -26402.335512
EM: Round [829] log likelihood: -26402.334897
EM: Round [830] log likelihood: -26402.334285
EM: Round [831] log likelihood: -26402.333678
EM: Round [832] log likelihood: -26402.333074
EM: Round [833] log likelihood: -26402.332474
EM: Round [834] log likelihood: -26402.331878
EM: Round [835] log likelihood: -26402.331285
EM: Round [836] log likelihood: -26402.330696
EM: Round [837] log likelihood: -26402.330111
EM: Round [838] log likelihood: -26402.329530
EM: Round [839] log likelihood: -26402.328952
EM: Round [840] log likelihood: -26402.328378
EM: Round [841] log likelihood: -26402.327808
EM: Round [842] log likelihood: -26402.327241
EM: Round [843] log likelihood: -26402.326678
EM: Round [844] log likelihood: -26402.326118
EM: Round [845] log likelihood: -26402.325562
EM: Round [846] log likelihood: -26402.325009
EM: Round [847] log likelihood: -26402.324460
EM: Round [848] log likelihood: -26402.323915
EM: Round [849] log likelihood: -26402.323372
EM: Round [850] log likelihood: -26402.322833
EM: Round [851] log likelihood: -26402.322298
EM: Round [852] log likelihood: -26402.321766
EM: Round [853] log likelihood: -26402.321237
EM: Round [854] log likelihood: -26402.320712
EM: Round [855] log likelihood: -26402.320190
EM: Round [856] log likelihood: -26402.319671
EM: Round [857] log likelihood: -26402.319155
EM: Round [858] log likelihood: -26402.318643
EM: Round [859] log likelihood: -26402.318134
EM: Round [860] log likelihood: -26402.317628
EM: Round [861] log likelihood: -26402.317125
EM: Round [862] log likelihood: -26402.316626
EM: Round [863] log likelihood: -26402.316130
EM: Round [864] log likelihood: -26402.315636
EM: Round [865] log likelihood: -26402.315146
EM: Round [866] log likelihood: -26402.314659
EM: Round [867] log likelihood: -26402.314175
EM: Round [868] log likelihood: -26402.313694
EM: Round [869] log likelihood: -26402.313216
EM: Round [870] log likelihood: -26402.312741
EM: Round [871] log likelihood: -26402.312269
EM: Round [872] log likelihood: -26402.311800
EM: Round [873] log likelihood: -26402.311334
EM: Round [874] log likelihood: -26402.310871
EM: Round [875] log likelihood: -26402.310411
EM: Round [876] log likelihood: -26402.309953
EM: Round [877] log likelihood: -26402.309499
EM: Round [878] log likelihood: -26402.309047
EM: Round [879] log likelihood: -26402.308598
EM: Round [880] log likelihood: -26402.308152
EM: Round [881] log likelihood: -26402.307709
EM: Round [882] log likelihood: -26402.307269
EM: Round [883] log likelihood: -26402.306831
EM: Round [884] log likelihood: -26402.306396
EM: Round [885] log likelihood: -26402.305964
EM: Round [886] log likelihood: -26402.305534
EM: Round [887] log likelihood: -26402.305107
EM: Round [888] log likelihood: -26402.304683
EM: Round [889] log likelihood: -26402.304262
EM: Round [890] log likelihood: -26402.303843
EM: Round [891] log likelihood: -26402.303426
EM: Round [892] log likelihood: -26402.303013
EM: Round [893] log likelihood: -26402.302602
EM: Round [894] log likelihood: -26402.302193
EM: Round [895] log likelihood: -26402.301787
EM: Round [896] log likelihood: -26402.301384
EM: Round [897] log likelihood: -26402.300983
EM: Round [898] log likelihood: -26402.300585
EM: Round [899] log likelihood: -26402.300189
EM: Round [900] log likelihood: -26402.299795
EM: Round [901] log likelihood: -26402.299404
EM: Round [902] log likelihood: -26402.299016
EM: Round [903] log likelihood: -26402.298630
EM: Round [904] log likelihood: -26402.298246
EM: Round [905] log likelihood: -26402.297865
EM: Round [906] log likelihood: -26402.297486
EM: Round [907] log likelihood: -26402.297109
EM: Round [908] log likelihood: -26402.296735
EM: Round [909] log likelihood: -26402.296363
EM: Round [910] log likelihood: -26402.295993
EM: Round [911] log likelihood: -26402.295626
EM: Round [912] log likelihood: -26402.295261
EM: Round [913] log likelihood: -26402.294898
EM: Round [914] log likelihood: -26402.294538
EM: Round [915] log likelihood: -26402.294180
EM: Round [916] log likelihood: -26402.293824
EM: Round [917] log likelihood: -26402.293470
EM: Round [918] log likelihood: -26402.293118
EM: Round [919] log likelihood: -26402.292769
EM: Round [920] log likelihood: -26402.292422
EM: Round [921] log likelihood: -26402.292076
EM: Round [922] log likelihood: -26402.291734
EM: Round [923] log likelihood: -26402.291393
EM: Round [924] log likelihood: -26402.291054
EM: Round [925] log likelihood: -26402.290717
EM: Round [926] log likelihood: -26402.290383
EM: Round [927] log likelihood: -26402.290051
EM: Round [928] log likelihood: -26402.289720
EM: Round [929] log likelihood: -26402.289392
EM: Round [930] log likelihood: -26402.289066
EM: Round [931] log likelihood: -26402.288741
EM: Round [932] log likelihood: -26402.288419
EM: Round [933] log likelihood: -26402.288099
EM: Round [934] log likelihood: -26402.287781
EM: Round [935] log likelihood: -26402.287464
EM: Round [936] log likelihood: -26402.287150
EM: Round [937] log likelihood: -26402.286838
EM: Round [938] log likelihood: -26402.286527
EM: Round [939] log likelihood: -26402.286219
EM: Round [940] log likelihood: -26402.285912
EM: Round [941] log likelihood: -26402.285607
EM: Round [942] log likelihood: -26402.285305
EM: Round [943] log likelihood: -26402.285004
EM: Round [944] log likelihood: -26402.284705
EM: Round [945] log likelihood: -26402.284407
EM: Round [946] log likelihood: -26402.284112
EM: Round [947] log likelihood: -26402.283818
EM: Round [948] log likelihood: -26402.283527
EM: Round [949] log likelihood: -26402.283237
EM: Round [950] log likelihood: -26402.282948
EM: Round [951] log likelihood: -26402.282662
EM: Round [952] log likelihood: -26402.282377
EM: Round [953] log likelihood: -26402.282095
EM: Round [954] log likelihood: -26402.281814
EM: Round [955] log likelihood: -26402.281534
EM: Round [956] log likelihood: -26402.281256
EM: Round [957] log likelihood: -26402.280981
EM: Round [958] log likelihood: -26402.280706
EM: Round [959] log likelihood: -26402.280434
EM: Round [960] log likelihood: -26402.280163
EM: Round [961] log likelihood: -26402.279894
EM: Round [962] log likelihood: -26402.279626
EM: Round [963] log likelihood: -26402.279360
EM: Round [964] log likelihood: -26402.279096
EM: Round [965] log likelihood: -26402.278833
EM: Round [966] log likelihood: -26402.278572
EM: Round [967] log likelihood: -26402.278313
EM: Round [968] log likelihood: -26402.278055
EM: Round [969] log likelihood: -26402.277799
EM: Round [970] log likelihood: -26402.277544
EM: Round [971] log likelihood: -26402.277291
EM: Round [972] log likelihood: -26402.277040
EM: Round [973] log likelihood: -26402.276790
EM: Round [974] log likelihood: -26402.276541
EM: Round [975] log likelihood: -26402.276294
EM: Round [976] log likelihood: -26402.276049
EM: Round [977] log likelihood: -26402.275805
EM: Round [978] log likelihood: -26402.275563
EM: Round [979] log likelihood: -26402.275322
EM: Round [980] log likelihood: -26402.275082
EM: Round [981] log likelihood: -26402.274844
EM: Round [982] log likelihood: -26402.274608
EM: Round [983] log likelihood: -26402.274373
EM: Round [984] log likelihood: -26402.274139
EM: Round [985] log likelihood: -26402.273907
EM: Round [986] log likelihood: -26402.273676
EM: Round [987] log likelihood: -26402.273447
EM: Round [988] log likelihood: -26402.273219
EM: Round [989] log likelihood: -26402.272993
EM: Round [990] log likelihood: -26402.272767
EM: Round [991] log likelihood: -26402.272544
EM: Round [992] log likelihood: -26402.272321
EM: Round [993] log likelihood: -26402.272100
EM: Round [994] log likelihood: -26402.271881
EM: Round [995] log likelihood: -26402.271662
EM: Round [996] log likelihood: -26402.271445
EM: Round [997] log likelihood: -26402.271230
EM: Round [998] log likelihood: -26402.271015
EM: Round [999] log likelihood: -26402.270802
EM: Round [1000] log likelihood: -26402.270590
EM: Round [1001] log likelihood: -26402.270380
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/659_rd-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -15107.140015
EM: Round [1] log likelihood: -15076.718302
EM: Round [2] log likelihood: -15076.681118
EM: Round [3] log likelihood: -15076.681027
EM: Stopping iterations at round 3 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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295903958
Execution Time = 6.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.NMeURXWyeZ/fi_workdir/microH.dat
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.NMeURXWyeZ/fi_workdir/microH.dat /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_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.NMeURXWyeZ/fi_workdir/microH.dat /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.NMeURXWyeZ --json_outfile /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.NMeURXWyeZ --json_outfile /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.NMeURXWyeZ/ctat_genome_lib_build_dir > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.NMeURXWyeZ/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory