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/e6/33afafac74c3a090289a821c27d944/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/d66879494ce966f2fdef3eee46ce1c/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/81791f1b6a856adf2a027f58dd6a2b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/81791f1b6a856adf2a027f58dd6a2b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/33afafac74c3a090289a821c27d944/659_dm4-T1-TRNA-1_B23WHTKLT4_1_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_dm4-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/cytoBand.txt
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.u6OmFZLRev/fi_workdir --reads "/tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 08:15:48 ..... started STAR run
Jun 08 08:15:48 ..... loading genome
Jun 08 08:17:25 ... generating Suffix Array index
Jun 08 08:21:11 ... completed Suffix Array index
Jun 08 08:21:11 ..... processing annotations GTF
Jun 08 08:21:11 ..... inserting junctions into the genome indices
Jun 08 08:22:12 ..... started mapping
Jun 08 08:39:41 ..... finished mapping
Jun 08 08:39:42 ..... started sorting BAM
Jun 08 08:39:42 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 23.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.u6OmFZLRev/fi_workdir --reads "/tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
08:39:46 : INFO : Done.
Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[820000] -done parsing /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 6018,
'per_id < 96' => 4143,
'low complexity anchor region' => 46,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 21,
' ** passed ** ' => 8740,
'seq-similar region overlap' => 3
};
-writing fusion junction support info.
Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[697000] -fusion SPANNING read extraction for scaff: TMPRSS2--ERG
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 6355,
'lacks exon overlap' => 4176
};
Execution Time = 0.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2410.042375
EM: Round [1] log likelihood: -2410.038336
EM: Round [2] log likelihood: -2410.034351
EM: Round [3] log likelihood: -2410.030420
EM: Round [4] log likelihood: -2410.026543
EM: Round [5] log likelihood: -2410.022719
EM: Round [6] log likelihood: -2410.018946
EM: Round [7] log likelihood: -2410.015224
EM: Round [8] log likelihood: -2410.011553
EM: Round [9] log likelihood: -2410.007931
EM: Round [10] log likelihood: -2410.004358
EM: Round [11] log likelihood: -2410.000833
EM: Round [12] log likelihood: -2409.997355
EM: Round [13] log likelihood: -2409.993924
EM: Round [14] log likelihood: -2409.990539
EM: Round [15] log likelihood: -2409.987200
EM: Round [16] log likelihood: -2409.983905
EM: Round [17] log likelihood: -2409.980654
EM: Round [18] log likelihood: -2409.977447
EM: Round [19] log likelihood: -2409.974282
EM: Round [20] log likelihood: -2409.971160
EM: Round [21] log likelihood: -2409.968079
EM: Round [22] log likelihood: -2409.965040
EM: Round [23] log likelihood: -2409.962040
EM: Round [24] log likelihood: -2409.959081
EM: Round [25] log likelihood: -2409.956160
EM: Round [26] log likelihood: -2409.953279
EM: Round [27] log likelihood: -2409.950435
EM: Round [28] log likelihood: -2409.947629
EM: Round [29] log likelihood: -2409.944861
EM: Round [30] log likelihood: -2409.942128
EM: Round [31] log likelihood: -2409.939432
EM: Round [32] log likelihood: -2409.936772
EM: Round [33] log likelihood: -2409.934146
EM: Round [34] log likelihood: -2409.931555
EM: Round [35] log likelihood: -2409.928998
EM: Round [36] log likelihood: -2409.926474
EM: Round [37] log likelihood: -2409.923984
EM: Round [38] log likelihood: -2409.921526
EM: Round [39] log likelihood: -2409.919101
EM: Round [40] log likelihood: -2409.916707
EM: Round [41] log likelihood: -2409.914344
EM: Round [42] log likelihood: -2409.912013
EM: Round [43] log likelihood: -2409.909711
EM: Round [44] log likelihood: -2409.907440
EM: Round [45] log likelihood: -2409.905199
EM: Round [46] log likelihood: -2409.902986
EM: Round [47] log likelihood: -2409.900803
EM: Round [48] log likelihood: -2409.898648
EM: Round [49] log likelihood: -2409.896521
EM: Round [50] log likelihood: -2409.894421
EM: Round [51] log likelihood: -2409.892349
EM: Round [52] log likelihood: -2409.890304
EM: Round [53] log likelihood: -2409.888285
EM: Round [54] log likelihood: -2409.886292
EM: Round [55] log likelihood: -2409.884325
EM: Round [56] log likelihood: -2409.882384
EM: Round [57] log likelihood: -2409.880468
EM: Round [58] log likelihood: -2409.878576
EM: Round [59] log likelihood: -2409.876709
EM: Round [60] log likelihood: -2409.874866
EM: Round [61] log likelihood: -2409.873047
EM: Round [62] log likelihood: -2409.871251
EM: Round [63] log likelihood: -2409.869478
EM: Round [64] log likelihood: -2409.867728
EM: Round [65] log likelihood: -2409.866001
EM: Round [66] log likelihood: -2409.864296
EM: Round [67] log likelihood: -2409.862612
EM: Round [68] log likelihood: -2409.860951
EM: Round [69] log likelihood: -2409.859311
EM: Round [70] log likelihood: -2409.857691
EM: Round [71] log likelihood: -2409.856093
EM: Round [72] log likelihood: -2409.854515
EM: Round [73] log likelihood: -2409.852957
EM: Round [74] log likelihood: -2409.851419
EM: Round [75] log likelihood: -2409.849901
EM: Round [76] log likelihood: -2409.848403
EM: Round [77] log likelihood: -2409.846923
EM: Round [78] log likelihood: -2409.845463
EM: Round [79] log likelihood: -2409.844021
EM: Round [80] log likelihood: -2409.842597
EM: Round [81] log likelihood: -2409.841192
EM: Round [82] log likelihood: -2409.839804
EM: Round [83] log likelihood: -2409.838434
EM: Round [84] log likelihood: -2409.837082
EM: Round [85] log likelihood: -2409.835747
EM: Round [86] log likelihood: -2409.834429
EM: Round [87] log likelihood: -2409.833127
EM: Round [88] log likelihood: -2409.831843
EM: Round [89] log likelihood: -2409.830574
EM: Round [90] log likelihood: -2409.829322
EM: Round [91] log likelihood: -2409.828086
EM: Round [92] log likelihood: -2409.826865
EM: Round [93] log likelihood: -2409.825660
EM: Round [94] log likelihood: -2409.824470
EM: Round [95] log likelihood: -2409.823295
EM: Round [96] log likelihood: -2409.822135
EM: Round [97] log likelihood: -2409.820990
EM: Round [98] log likelihood: -2409.819859
EM: Round [99] log likelihood: -2409.818743
EM: Round [100] log likelihood: -2409.817640
EM: Round [101] log likelihood: -2409.816552
EM: Round [102] log likelihood: -2409.815477
EM: Round [103] log likelihood: -2409.814417
EM: Round [104] log likelihood: -2409.813369
EM: Round [105] log likelihood: -2409.812335
EM: Round [106] log likelihood: -2409.811313
EM: Round [107] log likelihood: -2409.810305
EM: Round [108] log likelihood: -2409.809309
EM: Round [109] log likelihood: -2409.808326
EM: Round [110] log likelihood: -2409.807356
EM: Round [111] log likelihood: -2409.806397
EM: Round [112] log likelihood: -2409.805451
EM: Round [113] log likelihood: -2409.804517
EM: Round [114] log likelihood: -2409.803594
EM: Round [115] log likelihood: -2409.802683
EM: Round [116] log likelihood: -2409.801784
EM: Round [117] log likelihood: -2409.800895
EM: Round [118] log likelihood: -2409.800018
EM: Round [119] log likelihood: -2409.799152
EM: Round [120] log likelihood: -2409.798297
EM: Round [121] log likelihood: -2409.797453
EM: Round [122] log likelihood: -2409.796619
EM: Round [123] log likelihood: -2409.795796
EM: Round [124] log likelihood: -2409.794983
EM: Round [125] log likelihood: -2409.794180
EM: Round [126] log likelihood: -2409.793388
EM: Round [127] log likelihood: -2409.792605
EM: Round [128] log likelihood: -2409.791832
EM: Round [129] log likelihood: -2409.791069
EM: Round [130] log likelihood: -2409.790316
EM: Round [131] log likelihood: -2409.789571
EM: Round [132] log likelihood: -2409.788837
EM: Round [133] log likelihood: -2409.788111
EM: Round [134] log likelihood: -2409.787395
EM: Round [135] log likelihood: -2409.786687
EM: Round [136] log likelihood: -2409.785988
EM: Round [137] log likelihood: -2409.785299
EM: Round [138] log likelihood: -2409.784617
EM: Round [139] log likelihood: -2409.783945
EM: Round [140] log likelihood: -2409.783280
EM: Round [141] log likelihood: -2409.782624
EM: Round [142] log likelihood: -2409.781977
EM: Round [143] log likelihood: -2409.781337
EM: Round [144] log likelihood: -2409.780705
EM: Round [145] log likelihood: -2409.780081
EM: Round [146] log likelihood: -2409.779465
EM: Round [147] log likelihood: -2409.778857
EM: Round [148] log likelihood: -2409.778256
EM: Round [149] log likelihood: -2409.777663
EM: Round [150] log likelihood: -2409.777077
EM: Round [151] log likelihood: -2409.776499
EM: Round [152] log likelihood: -2409.775928
EM: Round [153] log likelihood: -2409.775364
EM: Round [154] log likelihood: -2409.774807
EM: Round [155] log likelihood: -2409.774256
EM: Round [156] log likelihood: -2409.773713
EM: Round [157] log likelihood: -2409.773177
EM: Round [158] log likelihood: -2409.772647
EM: Round [159] log likelihood: -2409.772124
EM: Round [160] log likelihood: -2409.771607
EM: Round [161] log likelihood: -2409.771097
EM: Round [162] log likelihood: -2409.770593
EM: Round [163] log likelihood: -2409.770095
EM: Round [164] log likelihood: -2409.769604
EM: Round [165] log likelihood: -2409.769119
EM: Round [166] log likelihood: -2409.768639
EM: Round [167] log likelihood: -2409.768166
EM: Round [168] log likelihood: -2409.767699
EM: Round [169] log likelihood: -2409.767237
EM: Round [170] log likelihood: -2409.766781
EM: Round [171] log likelihood: -2409.766331
EM: Round [172] log likelihood: -2409.765887
EM: Round [173] log likelihood: -2409.765448
EM: Round [174] log likelihood: -2409.765014
EM: Round [175] log likelihood: -2409.764586
EM: Round [176] log likelihood: -2409.764163
EM: Round [177] log likelihood: -2409.763746
EM: Round [178] log likelihood: -2409.763333
EM: Round [179] log likelihood: -2409.762926
EM: Round [180] log likelihood: -2409.762524
EM: Round [181] log likelihood: -2409.762127
EM: Round [182] log likelihood: -2409.761734
EM: Round [183] log likelihood: -2409.761347
EM: Round [184] log likelihood: -2409.760964
EM: Round [185] log likelihood: -2409.760587
EM: Round [186] log likelihood: -2409.760213
EM: Round [187] log likelihood: -2409.759845
EM: Round [188] log likelihood: -2409.759481
EM: Round [189] log likelihood: -2409.759122
EM: Round [190] log likelihood: -2409.758767
EM: Round [191] log likelihood: -2409.758416
EM: Round [192] log likelihood: -2409.758070
EM: Round [193] log likelihood: -2409.757728
EM: Round [194] log likelihood: -2409.757390
EM: Round [195] log likelihood: -2409.757057
EM: Round [196] log likelihood: -2409.756728
EM: Round [197] log likelihood: -2409.756402
EM: Round [198] log likelihood: -2409.756081
EM: Round [199] log likelihood: -2409.755764
EM: Round [200] log likelihood: -2409.755451
EM: Round [201] log likelihood: -2409.755141
EM: Round [202] log likelihood: -2409.754836
EM: Round [203] log likelihood: -2409.754534
EM: Round [204] log likelihood: -2409.754236
EM: Round [205] log likelihood: -2409.753942
EM: Round [206] log likelihood: -2409.753651
EM: Round [207] log likelihood: -2409.753364
EM: Round [208] log likelihood: -2409.753080
EM: Round [209] log likelihood: -2409.752800
EM: Round [210] log likelihood: -2409.752524
EM: Round [211] log likelihood: -2409.752250
EM: Round [212] log likelihood: -2409.751981
EM: Round [213] log likelihood: -2409.751714
EM: Round [214] log likelihood: -2409.751451
EM: Round [215] log likelihood: -2409.751191
EM: Round [216] log likelihood: -2409.750935
EM: Round [217] log likelihood: -2409.750681
EM: Round [218] log likelihood: -2409.750431
EM: Round [219] log likelihood: -2409.750184
EM: Round [220] log likelihood: -2409.749940
EM: Round [221] log likelihood: -2409.749698
EM: Round [222] log likelihood: -2409.749460
EM: Round [223] log likelihood: -2409.749225
EM: Round [224] log likelihood: -2409.748993
EM: Round [225] log likelihood: -2409.748763
EM: Round [226] log likelihood: -2409.748537
EM: Round [227] log likelihood: -2409.748313
EM: Round [228] log likelihood: -2409.748092
EM: Round [229] log likelihood: -2409.747874
EM: Round [230] log likelihood: -2409.747658
EM: Round [231] log likelihood: -2409.747445
EM: Round [232] log likelihood: -2409.747235
EM: Round [233] log likelihood: -2409.747027
EM: Round [234] log likelihood: -2409.746822
EM: Round [235] log likelihood: -2409.746619
EM: Round [236] log likelihood: -2409.746419
EM: Round [237] log likelihood: -2409.746222
EM: Round [238] log likelihood: -2409.746026
EM: Round [239] log likelihood: -2409.745834
EM: Round [240] log likelihood: -2409.745643
EM: Round [241] log likelihood: -2409.745455
EM: Round [242] log likelihood: -2409.745270
EM: Round [243] log likelihood: -2409.745086
EM: Round [244] log likelihood: -2409.744905
EM: Round [245] log likelihood: -2409.744726
EM: Round [246] log likelihood: -2409.744550
EM: Round [247] log likelihood: -2409.744375
EM: Round [248] log likelihood: -2409.744203
EM: Round [249] log likelihood: -2409.744032
EM: Round [250] log likelihood: -2409.743864
EM: Round [251] log likelihood: -2409.743698
EM: Round [252] log likelihood: -2409.743534
EM: Round [253] log likelihood: -2409.743372
EM: Round [254] log likelihood: -2409.743212
EM: Round [255] log likelihood: -2409.743054
EM: Round [256] log likelihood: -2409.742898
EM: Round [257] log likelihood: -2409.742744
EM: Round [258] log likelihood: -2409.742592
EM: Round [259] log likelihood: -2409.742442
EM: Round [260] log likelihood: -2409.742293
EM: Round [261] log likelihood: -2409.742147
EM: Round [262] log likelihood: -2409.742002
EM: Round [263] log likelihood: -2409.741859
EM: Round [264] log likelihood: -2409.741717
EM: Round [265] log likelihood: -2409.741578
EM: Round [266] log likelihood: -2409.741440
EM: Round [267] log likelihood: -2409.741304
EM: Round [268] log likelihood: -2409.741169
EM: Round [269] log likelihood: -2409.741037
EM: Round [270] log likelihood: -2409.740906
EM: Round [271] log likelihood: -2409.740776
EM: Round [272] log likelihood: -2409.740648
EM: Round [273] log likelihood: -2409.740522
EM: Round [274] log likelihood: -2409.740397
EM: Round [275] log likelihood: -2409.740274
EM: Round [276] log likelihood: -2409.740152
EM: Round [277] log likelihood: -2409.740032
EM: Round [278] log likelihood: -2409.739913
EM: Round [279] log likelihood: -2409.739796
EM: Round [280] log likelihood: -2409.739680
EM: Round [281] log likelihood: -2409.739566
EM: Round [282] log likelihood: -2409.739453
EM: Round [283] log likelihood: -2409.739341
EM: Round [284] log likelihood: -2409.739231
EM: Round [285] log likelihood: -2409.739122
EM: Round [286] log likelihood: -2409.739014
EM: Round [287] log likelihood: -2409.738908
EM: Round [288] log likelihood: -2409.738803
EM: Round [289] log likelihood: -2409.738700
EM: Round [290] log likelihood: -2409.738597
EM: Round [291] log likelihood: -2409.738496
EM: Round [292] log likelihood: -2409.738396
EM: Stopping iterations at round 292 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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir
-done, see /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1859.620900
EM: Round [1] log likelihood: -1859.620900
EM: Stopping iterations at round 1 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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 102160001
Execution Time = 1.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.u6OmFZLRev/fi_workdir/microH.dat
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.u6OmFZLRev/fi_workdir/microH.dat /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/fi_workdir/microH.dat /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.u6OmFZLRev --json_outfile /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_dm4-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.u6OmFZLRev --json_outfile /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_dm4-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_dm4-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_dm4-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.u6OmFZLRev/ctat_genome_lib_build_dir > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.u6OmFZLRev/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory