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/5a/421a8a1966fe647f3bcaa370826a0b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/421a8a1966fe647f3bcaa370826a0b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/dfea8092ca59d5e6e90122e6298c87/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/387af25a3a0e5e8d5bad9f24034cd9/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/387af25a3a0e5e8d5bad9f24034cd9/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv --gtf /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv --gtf /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/cytoBand.txt
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed
-parsing GTF file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --CPU 8 --out_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star --out_dir /tmp/nxf.ksoFEZ4fk5/fi_workdir --reads "/tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:26:54 ..... started STAR run
Jun 08 10:26:54 ..... loading genome
Jun 08 10:28:42 ... generating Suffix Array index
Jun 08 10:33:01 ... completed Suffix Array index
Jun 08 10:33:01 ..... processing annotations GTF
Jun 08 10:33:02 ..... inserting junctions into the genome indices
Jun 08 10:34:09 ..... started mapping
Jun 08 12:11:04 ..... finished mapping
Jun 08 12:11:06 ..... started sorting BAM
Jun 08 12:11:06 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
Execution Time = 104.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --CPU 8 --out_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star --out_dir /tmp/nxf.ksoFEZ4fk5/fi_workdir --reads "/tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --remove_dups
12:11:09 : INFO : Done.
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
-parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam
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[310000] -done parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 1786,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 72,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
'seq-similar region overlap' => 65,
'num genes matched < 2' => 20,
'excessive soft clipping' => 2693,
'small anchor length' => 36,
' ** passed ** ' => 3277
};
-writing fusion junction support info.
Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 4916,
'lacks exon overlap' => 1997
};
Execution Time = 0.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2892.601368
EM: Round [1] log likelihood: -2890.826180
EM: Round [2] log likelihood: -2890.817047
EM: Round [3] log likelihood: -2890.808458
EM: Round [4] log likelihood: -2890.800020
EM: Round [5] log likelihood: -2890.791728
EM: Round [6] log likelihood: -2890.783579
EM: Round [7] log likelihood: -2890.775569
EM: Round [8] log likelihood: -2890.767695
EM: Round [9] log likelihood: -2890.759953
EM: Round [10] log likelihood: -2890.752341
EM: Round [11] log likelihood: -2890.744854
EM: Round [12] log likelihood: -2890.737490
EM: Round [13] log likelihood: -2890.730247
EM: Round [14] log likelihood: -2890.723121
EM: Round [15] log likelihood: -2890.716109
EM: Round [16] log likelihood: -2890.709210
EM: Round [17] log likelihood: -2890.702420
EM: Round [18] log likelihood: -2890.695737
EM: Round [19] log likelihood: -2890.689158
EM: Round [20] log likelihood: -2890.682682
EM: Round [21] log likelihood: -2890.676306
EM: Round [22] log likelihood: -2890.670028
EM: Round [23] log likelihood: -2890.663845
EM: Round [24] log likelihood: -2890.657757
EM: Round [25] log likelihood: -2890.651760
EM: Round [26] log likelihood: -2890.645853
EM: Round [27] log likelihood: -2890.640034
EM: Round [28] log likelihood: -2890.634301
EM: Round [29] log likelihood: -2890.628652
EM: Round [30] log likelihood: -2890.623087
EM: Round [31] log likelihood: -2890.617602
EM: Round [32] log likelihood: -2890.612197
EM: Round [33] log likelihood: -2890.606869
EM: Round [34] log likelihood: -2890.601618
EM: Round [35] log likelihood: -2890.596442
EM: Round [36] log likelihood: -2890.591339
EM: Round [37] log likelihood: -2890.586309
EM: Round [38] log likelihood: -2890.581349
EM: Round [39] log likelihood: -2890.576458
EM: Round [40] log likelihood: -2890.571635
EM: Round [41] log likelihood: -2890.566879
EM: Round [42] log likelihood: -2890.562188
EM: Round [43] log likelihood: -2890.557562
EM: Round [44] log likelihood: -2890.552999
EM: Round [45] log likelihood: -2890.548498
EM: Round [46] log likelihood: -2890.544058
EM: Round [47] log likelihood: -2890.539677
EM: Round [48] log likelihood: -2890.535356
EM: Round [49] log likelihood: -2890.531091
EM: Round [50] log likelihood: -2890.526884
EM: Round [51] log likelihood: -2890.522732
EM: Round [52] log likelihood: -2890.518635
EM: Round [53] log likelihood: -2890.514592
EM: Round [54] log likelihood: -2890.510602
EM: Round [55] log likelihood: -2890.506664
EM: Round [56] log likelihood: -2890.502776
EM: Round [57] log likelihood: -2890.498939
EM: Round [58] log likelihood: -2890.495152
EM: Round [59] log likelihood: -2890.491413
EM: Round [60] log likelihood: -2890.487721
EM: Round [61] log likelihood: -2890.484077
EM: Round [62] log likelihood: -2890.480479
EM: Round [63] log likelihood: -2890.476927
EM: Round [64] log likelihood: -2890.473419
EM: Round [65] log likelihood: -2890.469955
EM: Round [66] log likelihood: -2890.466535
EM: Round [67] log likelihood: -2890.463157
EM: Round [68] log likelihood: -2890.459821
EM: Round [69] log likelihood: -2890.456526
EM: Round [70] log likelihood: -2890.453273
EM: Round [71] log likelihood: -2890.450059
EM: Round [72] log likelihood: -2890.446884
EM: Round [73] log likelihood: -2890.443749
EM: Round [74] log likelihood: -2890.440651
EM: Round [75] log likelihood: -2890.437592
EM: Round [76] log likelihood: -2890.434569
EM: Round [77] log likelihood: -2890.431583
EM: Round [78] log likelihood: -2890.428632
EM: Round [79] log likelihood: -2890.425718
EM: Round [80] log likelihood: -2890.422838
EM: Round [81] log likelihood: -2890.419992
EM: Round [82] log likelihood: -2890.417180
EM: Round [83] log likelihood: -2890.414402
EM: Round [84] log likelihood: -2890.411657
EM: Round [85] log likelihood: -2890.408944
EM: Round [86] log likelihood: -2890.406262
EM: Round [87] log likelihood: -2890.403613
EM: Round [88] log likelihood: -2890.400994
EM: Round [89] log likelihood: -2890.398406
EM: Round [90] log likelihood: -2890.395848
EM: Round [91] log likelihood: -2890.393320
EM: Round [92] log likelihood: -2890.390821
EM: Round [93] log likelihood: -2890.388352
EM: Round [94] log likelihood: -2890.385910
EM: Round [95] log likelihood: -2890.383497
EM: Round [96] log likelihood: -2890.381111
EM: Round [97] log likelihood: -2890.378753
EM: Round [98] log likelihood: -2890.376421
EM: Round [99] log likelihood: -2890.374117
EM: Round [100] log likelihood: -2890.371838
EM: Round [101] log likelihood: -2890.369585
EM: Round [102] log likelihood: -2890.367358
EM: Round [103] log likelihood: -2890.365156
EM: Round [104] log likelihood: -2890.362979
EM: Round [105] log likelihood: -2890.360826
EM: Round [106] log likelihood: -2890.358697
EM: Round [107] log likelihood: -2890.356592
EM: Round [108] log likelihood: -2890.354511
EM: Round [109] log likelihood: -2890.352453
EM: Round [110] log likelihood: -2890.350418
EM: Round [111] log likelihood: -2890.348405
EM: Round [112] log likelihood: -2890.346415
EM: Round [113] log likelihood: -2890.344447
EM: Round [114] log likelihood: -2890.342500
EM: Round [115] log likelihood: -2890.340575
EM: Round [116] log likelihood: -2890.338672
EM: Round [117] log likelihood: -2890.336789
EM: Round [118] log likelihood: -2890.334926
EM: Round [119] log likelihood: -2890.333084
EM: Round [120] log likelihood: -2890.331262
EM: Round [121] log likelihood: -2890.329460
EM: Round [122] log likelihood: -2890.327678
EM: Round [123] log likelihood: -2890.325915
EM: Round [124] log likelihood: -2890.324171
EM: Round [125] log likelihood: -2890.322446
EM: Round [126] log likelihood: -2890.320740
EM: Round [127] log likelihood: -2890.319052
EM: Round [128] log likelihood: -2890.317382
EM: Round [129] log likelihood: -2890.315730
EM: Round [130] log likelihood: -2890.314096
EM: Round [131] log likelihood: -2890.312479
EM: Round [132] log likelihood: -2890.310880
EM: Round [133] log likelihood: -2890.309297
EM: Round [134] log likelihood: -2890.307732
EM: Round [135] log likelihood: -2890.306183
EM: Round [136] log likelihood: -2890.304651
EM: Round [137] log likelihood: -2890.303135
EM: Round [138] log likelihood: -2890.301635
EM: Round [139] log likelihood: -2890.300151
EM: Round [140] log likelihood: -2890.298682
EM: Round [141] log likelihood: -2890.297229
EM: Round [142] log likelihood: -2890.295792
EM: Round [143] log likelihood: -2890.294369
EM: Round [144] log likelihood: -2890.292962
EM: Round [145] log likelihood: -2890.291569
EM: Round [146] log likelihood: -2890.290191
EM: Round [147] log likelihood: -2890.288827
EM: Round [148] log likelihood: -2890.287477
EM: Round [149] log likelihood: -2890.286142
EM: Round [150] log likelihood: -2890.284820
EM: Round [151] log likelihood: -2890.283513
EM: Round [152] log likelihood: -2890.282218
EM: Round [153] log likelihood: -2890.280938
EM: Round [154] log likelihood: -2890.279670
EM: Round [155] log likelihood: -2890.278416
EM: Round [156] log likelihood: -2890.277174
EM: Round [157] log likelihood: -2890.275946
EM: Round [158] log likelihood: -2890.274730
EM: Round [159] log likelihood: -2890.273526
EM: Round [160] log likelihood: -2890.272335
EM: Round [161] log likelihood: -2890.271157
EM: Round [162] log likelihood: -2890.269990
EM: Round [163] log likelihood: -2890.268835
EM: Round [164] log likelihood: -2890.267692
EM: Round [165] log likelihood: -2890.266561
EM: Round [166] log likelihood: -2890.265442
EM: Round [167] log likelihood: -2890.264333
EM: Round [168] log likelihood: -2890.263237
EM: Round [169] log likelihood: -2890.262151
EM: Round [170] log likelihood: -2890.261076
EM: Round [171] log likelihood: -2890.260012
EM: Round [172] log likelihood: -2890.258959
EM: Round [173] log likelihood: -2890.257917
EM: Round [174] log likelihood: -2890.256885
EM: Round [175] log likelihood: -2890.255864
EM: Round [176] log likelihood: -2890.254853
EM: Round [177] log likelihood: -2890.253852
EM: Round [178] log likelihood: -2890.252862
EM: Round [179] log likelihood: -2890.251881
EM: Round [180] log likelihood: -2890.250910
EM: Round [181] log likelihood: -2890.249949
EM: Round [182] log likelihood: -2890.248998
EM: Round [183] log likelihood: -2890.248056
EM: Round [184] log likelihood: -2890.247124
EM: Round [185] log likelihood: -2890.246201
EM: Round [186] log likelihood: -2890.245287
EM: Round [187] log likelihood: -2890.244382
EM: Round [188] log likelihood: -2890.243487
EM: Round [189] log likelihood: -2890.242600
EM: Round [190] log likelihood: -2890.241722
EM: Round [191] log likelihood: -2890.240853
EM: Round [192] log likelihood: -2890.239993
EM: Round [193] log likelihood: -2890.239141
EM: Round [194] log likelihood: -2890.238298
EM: Round [195] log likelihood: -2890.237463
EM: Round [196] log likelihood: -2890.236636
EM: Round [197] log likelihood: -2890.235817
EM: Round [198] log likelihood: -2890.235007
EM: Round [199] log likelihood: -2890.234205
EM: Round [200] log likelihood: -2890.233410
EM: Round [201] log likelihood: -2890.232624
EM: Round [202] log likelihood: -2890.231845
EM: Round [203] log likelihood: -2890.231074
EM: Round [204] log likelihood: -2890.230310
EM: Round [205] log likelihood: -2890.229554
EM: Round [206] log likelihood: -2890.228806
EM: Round [207] log likelihood: -2890.228065
EM: Round [208] log likelihood: -2890.227331
EM: Round [209] log likelihood: -2890.226604
EM: Round [210] log likelihood: -2890.225885
EM: Round [211] log likelihood: -2890.225172
EM: Round [212] log likelihood: -2890.224467
EM: Round [213] log likelihood: -2890.223768
EM: Round [214] log likelihood: -2890.223076
EM: Round [215] log likelihood: -2890.222391
EM: Round [216] log likelihood: -2890.221713
EM: Round [217] log likelihood: -2890.221041
EM: Round [218] log likelihood: -2890.220376
EM: Round [219] log likelihood: -2890.219718
EM: Round [220] log likelihood: -2890.219066
EM: Round [221] log likelihood: -2890.218420
EM: Round [222] log likelihood: -2890.217780
EM: Round [223] log likelihood: -2890.217147
EM: Round [224] log likelihood: -2890.216520
EM: Round [225] log likelihood: -2890.215899
EM: Round [226] log likelihood: -2890.215284
EM: Round [227] log likelihood: -2890.214675
EM: Round [228] log likelihood: -2890.214072
EM: Round [229] log likelihood: -2890.213474
EM: Round [230] log likelihood: -2890.212883
EM: Round [231] log likelihood: -2890.212297
EM: Round [232] log likelihood: -2890.211717
EM: Round [233] log likelihood: -2890.211143
EM: Round [234] log likelihood: -2890.210574
EM: Round [235] log likelihood: -2890.210010
EM: Round [236] log likelihood: -2890.209452
EM: Round [237] log likelihood: -2890.208900
EM: Round [238] log likelihood: -2890.208353
EM: Round [239] log likelihood: -2890.207811
EM: Round [240] log likelihood: -2890.207274
EM: Round [241] log likelihood: -2890.206742
EM: Round [242] log likelihood: -2890.206216
EM: Round [243] log likelihood: -2890.205694
EM: Round [244] log likelihood: -2890.205178
EM: Round [245] log likelihood: -2890.204667
EM: Round [246] log likelihood: -2890.204160
EM: Round [247] log likelihood: -2890.203658
EM: Round [248] log likelihood: -2890.203162
EM: Round [249] log likelihood: -2890.202669
EM: Round [250] log likelihood: -2890.202182
EM: Round [251] log likelihood: -2890.201699
EM: Round [252] log likelihood: -2890.201221
EM: Round [253] log likelihood: -2890.200748
EM: Round [254] log likelihood: -2890.200279
EM: Round [255] log likelihood: -2890.199815
EM: Round [256] log likelihood: -2890.199355
EM: Round [257] log likelihood: -2890.198899
EM: Round [258] log likelihood: -2890.198448
EM: Round [259] log likelihood: -2890.198001
EM: Round [260] log likelihood: -2890.197558
EM: Round [261] log likelihood: -2890.197120
EM: Round [262] log likelihood: -2890.196685
EM: Round [263] log likelihood: -2890.196255
EM: Round [264] log likelihood: -2890.195829
EM: Round [265] log likelihood: -2890.195407
EM: Round [266] log likelihood: -2890.194989
EM: Round [267] log likelihood: -2890.194575
EM: Round [268] log likelihood: -2890.194165
EM: Round [269] log likelihood: -2890.193759
EM: Round [270] log likelihood: -2890.193357
EM: Round [271] log likelihood: -2890.192958
EM: Round [272] log likelihood: -2890.192563
EM: Round [273] log likelihood: -2890.192173
EM: Round [274] log likelihood: -2890.191785
EM: Round [275] log likelihood: -2890.191402
EM: Round [276] log likelihood: -2890.191022
EM: Round [277] log likelihood: -2890.190645
EM: Round [278] log likelihood: -2890.190273
EM: Round [279] log likelihood: -2890.189903
EM: Round [280] log likelihood: -2890.189538
EM: Round [281] log likelihood: -2890.189175
EM: Round [282] log likelihood: -2890.188817
EM: Round [283] log likelihood: -2890.188461
EM: Round [284] log likelihood: -2890.188109
EM: Round [285] log likelihood: -2890.187760
EM: Round [286] log likelihood: -2890.187415
EM: Round [287] log likelihood: -2890.187073
EM: Round [288] log likelihood: -2890.186734
EM: Round [289] log likelihood: -2890.186398
EM: Round [290] log likelihood: -2890.186065
EM: Round [291] log likelihood: -2890.185736
EM: Round [292] log likelihood: -2890.185409
EM: Round [293] log likelihood: -2890.185086
EM: Round [294] log likelihood: -2890.184766
EM: Round [295] log likelihood: -2890.184449
EM: Round [296] log likelihood: -2890.184134
EM: Round [297] log likelihood: -2890.183823
EM: Round [298] log likelihood: -2890.183515
EM: Round [299] log likelihood: -2890.183209
EM: Round [300] log likelihood: -2890.182907
EM: Round [301] log likelihood: -2890.182607
EM: Round [302] log likelihood: -2890.182310
EM: Round [303] log likelihood: -2890.182016
EM: Round [304] log likelihood: -2890.181725
EM: Round [305] log likelihood: -2890.181436
EM: Round [306] log likelihood: -2890.181150
EM: Round [307] log likelihood: -2890.180867
EM: Round [308] log likelihood: -2890.180586
EM: Round [309] log likelihood: -2890.180308
EM: Round [310] log likelihood: -2890.180033
EM: Round [311] log likelihood: -2890.179760
EM: Round [312] log likelihood: -2890.179490
EM: Round [313] log likelihood: -2890.179222
EM: Round [314] log likelihood: -2890.178957
EM: Round [315] log likelihood: -2890.178695
EM: Round [316] log likelihood: -2890.178434
EM: Round [317] log likelihood: -2890.178177
EM: Round [318] log likelihood: -2890.177921
EM: Round [319] log likelihood: -2890.177668
EM: Round [320] log likelihood: -2890.177418
EM: Round [321] log likelihood: -2890.177169
EM: Round [322] log likelihood: -2890.176923
EM: Round [323] log likelihood: -2890.176680
EM: Round [324] log likelihood: -2890.176438
EM: Round [325] log likelihood: -2890.176199
EM: Round [326] log likelihood: -2890.175962
EM: Round [327] log likelihood: -2890.175728
EM: Round [328] log likelihood: -2890.175495
EM: Round [329] log likelihood: -2890.175265
EM: Round [330] log likelihood: -2890.175037
EM: Round [331] log likelihood: -2890.174811
EM: Round [332] log likelihood: -2890.174587
EM: Round [333] log likelihood: -2890.174365
EM: Round [334] log likelihood: -2890.174145
EM: Round [335] log likelihood: -2890.173927
EM: Round [336] log likelihood: -2890.173712
EM: Round [337] log likelihood: -2890.173498
EM: Round [338] log likelihood: -2890.173286
EM: Round [339] log likelihood: -2890.173077
EM: Round [340] log likelihood: -2890.172869
EM: Round [341] log likelihood: -2890.172663
EM: Round [342] log likelihood: -2890.172459
EM: Round [343] log likelihood: -2890.172257
EM: Round [344] log likelihood: -2890.172057
EM: Round [345] log likelihood: -2890.171859
EM: Round [346] log likelihood: -2890.171662
EM: Round [347] log likelihood: -2890.171468
EM: Round [348] log likelihood: -2890.171275
EM: Round [349] log likelihood: -2890.171084
EM: Round [350] log likelihood: -2890.170895
EM: Round [351] log likelihood: -2890.170707
EM: Round [352] log likelihood: -2890.170521
EM: Round [353] log likelihood: -2890.170337
EM: Round [354] log likelihood: -2890.170155
EM: Round [355] log likelihood: -2890.169974
EM: Round [356] log likelihood: -2890.169796
EM: Round [357] log likelihood: -2890.169618
EM: Round [358] log likelihood: -2890.169443
EM: Round [359] log likelihood: -2890.169269
EM: Round [360] log likelihood: -2890.169096
EM: Round [361] log likelihood: -2890.168925
EM: Round [362] log likelihood: -2890.168756
EM: Round [363] log likelihood: -2890.168589
EM: Round [364] log likelihood: -2890.168423
EM: Round [365] log likelihood: -2890.168258
EM: Round [366] log likelihood: -2890.168095
EM: Round [367] log likelihood: -2890.167933
EM: Round [368] log likelihood: -2890.167773
EM: Round [369] log likelihood: -2890.167615
EM: Round [370] log likelihood: -2890.167458
EM: Round [371] log likelihood: -2890.167302
EM: Round [372] log likelihood: -2890.167148
EM: Round [373] log likelihood: -2890.166995
EM: Round [374] log likelihood: -2890.166844
EM: Round [375] log likelihood: -2890.166694
EM: Round [376] log likelihood: -2890.166546
EM: Round [377] log likelihood: -2890.166398
EM: Round [378] log likelihood: -2890.166253
EM: Round [379] log likelihood: -2890.166108
EM: Round [380] log likelihood: -2890.165965
EM: Round [381] log likelihood: -2890.165823
EM: Round [382] log likelihood: -2890.165683
EM: Round [383] log likelihood: -2890.165544
EM: Round [384] log likelihood: -2890.165406
EM: Round [385] log likelihood: -2890.165269
EM: Round [386] log likelihood: -2890.165134
EM: Round [387] log likelihood: -2890.165000
EM: Round [388] log likelihood: -2890.164867
EM: Round [389] log likelihood: -2890.164735
EM: Round [390] log likelihood: -2890.164605
EM: Round [391] log likelihood: -2890.164475
EM: Round [392] log likelihood: -2890.164347
EM: Round [393] log likelihood: -2890.164220
EM: Round [394] log likelihood: -2890.164095
EM: Round [395] log likelihood: -2890.163970
EM: Round [396] log likelihood: -2890.163847
EM: Round [397] log likelihood: -2890.163725
EM: Round [398] log likelihood: -2890.163604
EM: Round [399] log likelihood: -2890.163484
EM: Round [400] log likelihood: -2890.163365
EM: Round [401] log likelihood: -2890.163247
EM: Round [402] log likelihood: -2890.163130
EM: Round [403] log likelihood: -2890.163015
EM: Round [404] log likelihood: -2890.162900
EM: Round [405] log likelihood: -2890.162786
EM: Round [406] log likelihood: -2890.162674
EM: Round [407] log likelihood: -2890.162563
EM: Round [408] log likelihood: -2890.162452
EM: Round [409] log likelihood: -2890.162343
EM: Round [410] log likelihood: -2890.162234
EM: Round [411] log likelihood: -2890.162127
EM: Round [412] log likelihood: -2890.162021
EM: Round [413] log likelihood: -2890.161915
EM: Round [414] log likelihood: -2890.161811
EM: Round [415] log likelihood: -2890.161707
EM: Round [416] log likelihood: -2890.161605
EM: Round [417] log likelihood: -2890.161503
EM: Round [418] log likelihood: -2890.161403
EM: Round [419] log likelihood: -2890.161303
EM: Stopping iterations at round 419 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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam"
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam into /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2645.228701
EM: Round [1] log likelihood: -2645.073177
EM: Round [2] log likelihood: -2645.072982
EM: Round [3] log likelihood: -2645.072982
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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz: 295366080
Execution Time = 6.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/fi_workdir/microH.dat
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ksoFEZ4fk5/fi_workdir/microH.dat /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/microH.dat /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ksoFEZ4fk5 --json_outfile /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ksoFEZ4fk5 --json_outfile /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2
Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --input_file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 --html_output /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --input_file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 --html_output /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [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 [ENSG00000242193.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory