Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/e1d6b42c01d96cc04a6c54a689e0b9/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/a2ac3cb18c4f8a05c8495de3625056/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/a2ac3cb18c4f8a05c8495de3625056/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/e1d6b42c01d96cc04a6c54a689e0b9/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/6519ad5518a0e0bd4ce875a1237308/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/cytoBand.txt
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.dkJEPjqjJR/fi_workdir --reads "/tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:58:12 ..... started STAR run
Jun 08 10:58:12 ..... loading genome
Jun 08 10:59:18 ... generating Suffix Array index
Jun 08 11:03:01 ... completed Suffix Array index
Jun 08 11:03:01 ..... processing annotations GTF
Jun 08 11:03:01 ..... inserting junctions into the genome indices
Jun 08 11:03:45 ..... started mapping
Jun 08 11:45:07 ..... finished mapping
Jun 08 11:45:08 ..... started sorting BAM
Jun 08 11:45:13 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 47.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.dkJEPjqjJR/fi_workdir --reads "/tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:46:21 : INFO : Done.
Execution Time = 0.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[17430000] -done parsing /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 16,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 68,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 27,
'num_hits: 8 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 48396,
'excessive soft clipping' => 98386,
' ** passed ** ' => 42136,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4930,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 318283,
'low complexity anchor region' => 39,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6351,
'exons hit < 2' => 2,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 18,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 625,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1222,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 6,
'num genes matched < 2' => 390,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 162,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 30356,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 556,
'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 77,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 15606,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 11037,
'num_hits: 9 != num_counted_on_fusion_contigs 6 ' => 18,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 5,
'per_id < 96' => 77880,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 14476,
'num_hits: 9 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 10 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 654,
'small anchor length' => 597,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 288,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 30,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 11170,
'seq-similar region overlap' => 5,
'num_hits: 7 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 42,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 110
};
-writing fusion junction support info.
Execution Time = 7.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: AC090572.2--CNBD1
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[5017000] -fusion SPANNING read extraction for scaff: COL1A1--SLC45A4
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[26000] -fusion SPANNING read extraction for scaff: FBXO25--AL669831.1
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[44000] -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6
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[6074000]
[6075000] -fusion SPANNING read extraction for scaff: MYB--NFIB
[1000]
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[42000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
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[47000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
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[53000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[79000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[74000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[68000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[50000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
[1000]
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[41000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[5305000] -fusion SPANNING read extraction for scaff: PRB3--MTRNR2L12
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[113000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[70000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[23000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[50000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 28512,
'lacks exon overlap' => 9538
};
Execution Time = 17.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -16366.880708
EM: Round [1] log likelihood: -16364.488195
EM: Round [2] log likelihood: -16364.163584
EM: Round [3] log likelihood: -16364.082508
EM: Round [4] log likelihood: -16364.051697
EM: Round [5] log likelihood: -16364.035801
EM: Round [6] log likelihood: -16364.025411
EM: Round [7] log likelihood: -16364.017369
EM: Round [8] log likelihood: -16364.010426
EM: Round [9] log likelihood: -16364.004029
EM: Round [10] log likelihood: -16363.997920
EM: Round [11] log likelihood: -16363.991972
EM: Round [12] log likelihood: -16363.986123
EM: Round [13] log likelihood: -16363.980343
EM: Round [14] log likelihood: -16363.974614
EM: Round [15] log likelihood: -16363.968929
EM: Round [16] log likelihood: -16363.963284
EM: Round [17] log likelihood: -16363.957677
EM: Round [18] log likelihood: -16363.952106
EM: Round [19] log likelihood: -16363.946570
EM: Round [20] log likelihood: -16363.941068
EM: Round [21] log likelihood: -16363.935600
EM: Round [22] log likelihood: -16363.930166
EM: Round [23] log likelihood: -16363.924766
EM: Round [24] log likelihood: -16363.919398
EM: Round [25] log likelihood: -16363.914062
EM: Round [26] log likelihood: -16363.908759
EM: Round [27] log likelihood: -16363.903487
EM: Round [28] log likelihood: -16363.898246
EM: Round [29] log likelihood: -16363.893036
EM: Round [30] log likelihood: -16363.887857
EM: Round [31] log likelihood: -16363.882709
EM: Round [32] log likelihood: -16363.877590
EM: Round [33] log likelihood: -16363.872500
EM: Round [34] log likelihood: -16363.867441
EM: Round [35] log likelihood: -16363.862410
EM: Round [36] log likelihood: -16363.857407
EM: Round [37] log likelihood: -16363.852434
EM: Round [38] log likelihood: -16363.847488
EM: Round [39] log likelihood: -16363.842570
EM: Round [40] log likelihood: -16363.837679
EM: Round [41] log likelihood: -16363.832816
EM: Round [42] log likelihood: -16363.827979
EM: Round [43] log likelihood: -16363.823170
EM: Round [44] log likelihood: -16363.818386
EM: Round [45] log likelihood: -16363.813629
EM: Round [46] log likelihood: -16363.808897
EM: Round [47] log likelihood: -16363.804191
EM: Round [48] log likelihood: -16363.799511
EM: Round [49] log likelihood: -16363.794855
EM: Round [50] log likelihood: -16363.790224
EM: Round [51] log likelihood: -16363.785618
EM: Round [52] log likelihood: -16363.781036
EM: Round [53] log likelihood: -16363.776479
EM: Round [54] log likelihood: -16363.771945
EM: Round [55] log likelihood: -16363.767434
EM: Round [56] log likelihood: -16363.762947
EM: Round [57] log likelihood: -16363.758483
EM: Round [58] log likelihood: -16363.754043
EM: Round [59] log likelihood: -16363.749624
EM: Round [60] log likelihood: -16363.745229
EM: Round [61] log likelihood: -16363.740855
EM: Round [62] log likelihood: -16363.736504
EM: Round [63] log likelihood: -16363.732175
EM: Round [64] log likelihood: -16363.727867
EM: Round [65] log likelihood: -16363.723581
EM: Round [66] log likelihood: -16363.719316
EM: Round [67] log likelihood: -16363.715072
EM: Round [68] log likelihood: -16363.710849
EM: Round [69] log likelihood: -16363.706647
EM: Round [70] log likelihood: -16363.702465
EM: Round [71] log likelihood: -16363.698303
EM: Round [72] log likelihood: -16363.694162
EM: Round [73] log likelihood: -16363.690040
EM: Round [74] log likelihood: -16363.685939
EM: Round [75] log likelihood: -16363.681857
EM: Round [76] log likelihood: -16363.677794
EM: Round [77] log likelihood: -16363.673751
EM: Round [78] log likelihood: -16363.669727
EM: Round [79] log likelihood: -16363.665721
EM: Round [80] log likelihood: -16363.661735
EM: Round [81] log likelihood: -16363.657767
EM: Round [82] log likelihood: -16363.653817
EM: Round [83] log likelihood: -16363.649886
EM: Round [84] log likelihood: -16363.645973
EM: Round [85] log likelihood: -16363.642078
EM: Round [86] log likelihood: -16363.638201
EM: Round [87] log likelihood: -16363.634341
EM: Round [88] log likelihood: -16363.630499
EM: Round [89] log likelihood: -16363.626674
EM: Round [90] log likelihood: -16363.622867
EM: Round [91] log likelihood: -16363.619076
EM: Round [92] log likelihood: -16363.615303
EM: Round [93] log likelihood: -16363.611546
EM: Round [94] log likelihood: -16363.607806
EM: Round [95] log likelihood: -16363.604083
EM: Round [96] log likelihood: -16363.600376
EM: Round [97] log likelihood: -16363.596685
EM: Round [98] log likelihood: -16363.593010
EM: Round [99] log likelihood: -16363.589352
EM: Round [100] log likelihood: -16363.585709
EM: Round [101] log likelihood: -16363.582082
EM: Round [102] log likelihood: -16363.578471
EM: Round [103] log likelihood: -16363.574875
EM: Round [104] log likelihood: -16363.571294
EM: Round [105] log likelihood: -16363.567729
EM: Round [106] log likelihood: -16363.564179
EM: Round [107] log likelihood: -16363.560644
EM: Round [108] log likelihood: -16363.557124
EM: Round [109] log likelihood: -16363.553619
EM: Round [110] log likelihood: -16363.550128
EM: Round [111] log likelihood: -16363.546652
EM: Round [112] log likelihood: -16363.543190
EM: Round [113] log likelihood: -16363.539743
EM: Round [114] log likelihood: -16363.536310
EM: Round [115] log likelihood: -16363.532891
EM: Round [116] log likelihood: -16363.529486
EM: Round [117] log likelihood: -16363.526095
EM: Round [118] log likelihood: -16363.522718
EM: Round [119] log likelihood: -16363.519355
EM: Round [120] log likelihood: -16363.516005
EM: Round [121] log likelihood: -16363.512669
EM: Round [122] log likelihood: -16363.509346
EM: Round [123] log likelihood: -16363.506036
EM: Round [124] log likelihood: -16363.502740
EM: Round [125] log likelihood: -16363.499457
EM: Round [126] log likelihood: -16363.496187
EM: Round [127] log likelihood: -16363.492929
EM: Round [128] log likelihood: -16363.489685
EM: Round [129] log likelihood: -16363.486453
EM: Round [130] log likelihood: -16363.483234
EM: Round [131] log likelihood: -16363.480028
EM: Round [132] log likelihood: -16363.476834
EM: Round [133] log likelihood: -16363.473653
EM: Round [134] log likelihood: -16363.470483
EM: Round [135] log likelihood: -16363.467326
EM: Round [136] log likelihood: -16363.464181
EM: Round [137] log likelihood: -16363.461049
EM: Round [138] log likelihood: -16363.457928
EM: Round [139] log likelihood: -16363.454819
EM: Round [140] log likelihood: -16363.451722
EM: Round [141] log likelihood: -16363.448636
EM: Round [142] log likelihood: -16363.445562
EM: Round [143] log likelihood: -16363.442500
EM: Round [144] log likelihood: -16363.439449
EM: Round [145] log likelihood: -16363.436410
EM: Round [146] log likelihood: -16363.433382
EM: Round [147] log likelihood: -16363.430365
EM: Round [148] log likelihood: -16363.427359
EM: Round [149] log likelihood: -16363.424365
EM: Round [150] log likelihood: -16363.421381
EM: Round [151] log likelihood: -16363.418409
EM: Round [152] log likelihood: -16363.415447
EM: Round [153] log likelihood: -16363.412496
EM: Round [154] log likelihood: -16363.409556
EM: Round [155] log likelihood: -16363.406626
EM: Round [156] log likelihood: -16363.403708
EM: Round [157] log likelihood: -16363.400799
EM: Round [158] log likelihood: -16363.397901
EM: Round [159] log likelihood: -16363.395014
EM: Round [160] log likelihood: -16363.392137
EM: Round [161] log likelihood: -16363.389270
EM: Round [162] log likelihood: -16363.386413
EM: Round [163] log likelihood: -16363.383566
EM: Round [164] log likelihood: -16363.380730
EM: Round [165] log likelihood: -16363.377903
EM: Round [166] log likelihood: -16363.375087
EM: Round [167] log likelihood: -16363.372280
EM: Round [168] log likelihood: -16363.369483
EM: Round [169] log likelihood: -16363.366696
EM: Round [170] log likelihood: -16363.363918
EM: Round [171] log likelihood: -16363.361151
EM: Round [172] log likelihood: -16363.358392
EM: Round [173] log likelihood: -16363.355644
EM: Round [174] log likelihood: -16363.352904
EM: Round [175] log likelihood: -16363.350174
EM: Round [176] log likelihood: -16363.347454
EM: Round [177] log likelihood: -16363.344742
EM: Round [178] log likelihood: -16363.342040
EM: Round [179] log likelihood: -16363.339347
EM: Round [180] log likelihood: -16363.336663
EM: Round [181] log likelihood: -16363.333989
EM: Round [182] log likelihood: -16363.331323
EM: Round [183] log likelihood: -16363.328666
EM: Round [184] log likelihood: -16363.326018
EM: Round [185] log likelihood: -16363.323379
EM: Round [186] log likelihood: -16363.320749
EM: Round [187] log likelihood: -16363.318127
EM: Round [188] log likelihood: -16363.315514
EM: Round [189] log likelihood: -16363.312910
EM: Round [190] log likelihood: -16363.310314
EM: Round [191] log likelihood: -16363.307727
EM: Round [192] log likelihood: -16363.305148
EM: Round [193] log likelihood: -16363.302578
EM: Round [194] log likelihood: -16363.300016
EM: Round [195] log likelihood: -16363.297463
EM: Round [196] log likelihood: -16363.294917
EM: Round [197] log likelihood: -16363.292380
EM: Round [198] log likelihood: -16363.289851
EM: Round [199] log likelihood: -16363.287331
EM: Round [200] log likelihood: -16363.284818
EM: Round [201] log likelihood: -16363.282313
EM: Round [202] log likelihood: -16363.279817
EM: Round [203] log likelihood: -16363.277328
EM: Round [204] log likelihood: -16363.274848
EM: Round [205] log likelihood: -16363.272375
EM: Round [206] log likelihood: -16363.269910
EM: Round [207] log likelihood: -16363.267452
EM: Round [208] log likelihood: -16363.265003
EM: Round [209] log likelihood: -16363.262561
EM: Round [210] log likelihood: -16363.260127
EM: Round [211] log likelihood: -16363.257700
EM: Round [212] log likelihood: -16363.255281
EM: Round [213] log likelihood: -16363.252870
EM: Round [214] log likelihood: -16363.250466
EM: Round [215] log likelihood: -16363.248069
EM: Round [216] log likelihood: -16363.245680
EM: Round [217] log likelihood: -16363.243299
EM: Round [218] log likelihood: -16363.240924
EM: Round [219] log likelihood: -16363.238557
EM: Round [220] log likelihood: -16363.236197
EM: Round [221] log likelihood: -16363.233844
EM: Round [222] log likelihood: -16363.231499
EM: Round [223] log likelihood: -16363.229160
EM: Round [224] log likelihood: -16363.226829
EM: Round [225] log likelihood: -16363.224504
EM: Round [226] log likelihood: -16363.222187
EM: Round [227] log likelihood: -16363.219877
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EM: Round [688] log likelihood: -16362.573284
EM: Round [689] log likelihood: -16362.572409
EM: Round [690] log likelihood: -16362.571536
EM: Round [691] log likelihood: -16362.570664
EM: Round [692] log likelihood: -16362.569793
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EM: Round [695] log likelihood: -16362.567190
EM: Round [696] log likelihood: -16362.566325
EM: Round [697] log likelihood: -16362.565461
EM: Round [698] log likelihood: -16362.564599
EM: Round [699] log likelihood: -16362.563738
EM: Round [700] log likelihood: -16362.562878
EM: Round [701] log likelihood: -16362.562020
EM: Round [702] log likelihood: -16362.561163
EM: Round [703] log likelihood: -16362.560307
EM: Round [704] log likelihood: -16362.559453
EM: Round [705] log likelihood: -16362.558600
EM: Round [706] log likelihood: -16362.557748
EM: Round [707] log likelihood: -16362.556898
EM: Round [708] log likelihood: -16362.556049
EM: Round [709] log likelihood: -16362.555201
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EM: Round [711] log likelihood: -16362.553510
EM: Round [712] log likelihood: -16362.552666
EM: Round [713] log likelihood: -16362.551823
EM: Round [714] log likelihood: -16362.550982
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EM: Round [716] log likelihood: -16362.549304
EM: Round [717] log likelihood: -16362.548466
EM: Round [718] log likelihood: -16362.547630
EM: Round [719] log likelihood: -16362.546795
EM: Round [720] log likelihood: -16362.545962
EM: Round [721] log likelihood: -16362.545130
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EM: Round [723] log likelihood: -16362.543469
EM: Round [724] log likelihood: -16362.542641
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EM: Round [726] log likelihood: -16362.540988
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EM: Round [731] log likelihood: -16362.536877
EM: Round [732] log likelihood: -16362.536059
EM: Round [733] log likelihood: -16362.535242
EM: Round [734] log likelihood: -16362.534426
EM: Round [735] log likelihood: -16362.533611
EM: Round [736] log likelihood: -16362.532798
EM: Round [737] log likelihood: -16362.531985
EM: Round [738] log likelihood: -16362.531174
EM: Round [739] log likelihood: -16362.530365
EM: Round [740] log likelihood: -16362.529556
EM: Round [741] log likelihood: -16362.528749
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EM: Round [743] log likelihood: -16362.527138
EM: Round [744] log likelihood: -16362.526334
EM: Round [745] log likelihood: -16362.525532
EM: Round [746] log likelihood: -16362.524730
EM: Round [747] log likelihood: -16362.523930
EM: Round [748] log likelihood: -16362.523132
EM: Round [749] log likelihood: -16362.522334
EM: Round [750] log likelihood: -16362.521537
EM: Round [751] log likelihood: -16362.520742
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EM: Round [753] log likelihood: -16362.519155
EM: Round [754] log likelihood: -16362.518363
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EM: Round [758] log likelihood: -16362.515208
EM: Round [759] log likelihood: -16362.514422
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EM: Round [761] log likelihood: -16362.512854
EM: Round [762] log likelihood: -16362.512072
EM: Round [763] log likelihood: -16362.511291
EM: Round [764] log likelihood: -16362.510511
EM: Round [765] log likelihood: -16362.509732
EM: Round [766] log likelihood: -16362.508954
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EM: Round [769] log likelihood: -16362.506627
EM: Round [770] log likelihood: -16362.505854
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EM: Round [774] log likelihood: -16362.502773
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EM: Round [776] log likelihood: -16362.501239
EM: Round [777] log likelihood: -16362.500474
EM: Round [778] log likelihood: -16362.499710
EM: Round [779] log likelihood: -16362.498947
EM: Round [780] log likelihood: -16362.498185
EM: Round [781] log likelihood: -16362.497424
EM: Round [782] log likelihood: -16362.496664
EM: Round [783] log likelihood: -16362.495906
EM: Round [784] log likelihood: -16362.495148
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EM: Round [786] log likelihood: -16362.493636
EM: Round [787] log likelihood: -16362.492882
EM: Round [788] log likelihood: -16362.492129
EM: Round [789] log likelihood: -16362.491377
EM: Round [790] log likelihood: -16362.490626
EM: Round [791] log likelihood: -16362.489876
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EM: Round [793] log likelihood: -16362.488380
EM: Round [794] log likelihood: -16362.487634
EM: Round [795] log likelihood: -16362.486888
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EM: Round [797] log likelihood: -16362.485400
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EM: Round [799] log likelihood: -16362.483917
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EM: Round [803] log likelihood: -16362.480963
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EM: Round [807] log likelihood: -16362.478025
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EM: Round [811] log likelihood: -16362.475105
EM: Round [812] log likelihood: -16362.474377
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EM: Round [814] log likelihood: -16362.472926
EM: Round [815] log likelihood: -16362.472201
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EM: Round [819] log likelihood: -16362.469314
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EM: Round [821] log likelihood: -16362.467876
EM: Round [822] log likelihood: -16362.467159
EM: Round [823] log likelihood: -16362.466443
EM: Round [824] log likelihood: -16362.465728
EM: Round [825] log likelihood: -16362.465013
EM: Round [826] log likelihood: -16362.464300
EM: Round [827] log likelihood: -16362.463588
EM: Round [828] log likelihood: -16362.462877
EM: Round [829] log likelihood: -16362.462167
EM: Round [830] log likelihood: -16362.461458
EM: Round [831] log likelihood: -16362.460749
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EM: Round [833] log likelihood: -16362.459336
EM: Round [834] log likelihood: -16362.458631
EM: Round [835] log likelihood: -16362.457927
EM: Round [836] log likelihood: -16362.457223
EM: Round [837] log likelihood: -16362.456521
EM: Round [838] log likelihood: -16362.455820
EM: Round [839] log likelihood: -16362.455120
EM: Round [840] log likelihood: -16362.454420
EM: Round [841] log likelihood: -16362.453722
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EM: Round [843] log likelihood: -16362.452328
EM: Round [844] log likelihood: -16362.451633
EM: Round [845] log likelihood: -16362.450938
EM: Round [846] log likelihood: -16362.450245
EM: Round [847] log likelihood: -16362.449552
EM: Round [848] log likelihood: -16362.448861
EM: Round [849] log likelihood: -16362.448170
EM: Round [850] log likelihood: -16362.447481
EM: Round [851] log likelihood: -16362.446792
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EM: Round [853] log likelihood: -16362.445418
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EM: Round [856] log likelihood: -16362.443363
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EM: Round [863] log likelihood: -16362.438602
EM: Round [864] log likelihood: -16362.437926
EM: Round [865] log likelihood: -16362.437250
EM: Round [866] log likelihood: -16362.436576
EM: Round [867] log likelihood: -16362.435902
EM: Round [868] log likelihood: -16362.435230
EM: Round [869] log likelihood: -16362.434558
EM: Round [870] log likelihood: -16362.433887
EM: Round [871] log likelihood: -16362.433217
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EM: Round [873] log likelihood: -16362.431880
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EM: Round [876] log likelihood: -16362.429881
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EM: Round [879] log likelihood: -16362.427890
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EM: Round [881] log likelihood: -16362.426568
EM: Round [882] log likelihood: -16362.425908
EM: Round [883] log likelihood: -16362.425249
EM: Round [884] log likelihood: -16362.424591
EM: Round [885] log likelihood: -16362.423933
EM: Round [886] log likelihood: -16362.423277
EM: Round [887] log likelihood: -16362.422622
EM: Round [888] log likelihood: -16362.421967
EM: Round [889] log likelihood: -16362.421313
EM: Round [890] log likelihood: -16362.420660
EM: Round [891] log likelihood: -16362.420009
EM: Round [892] log likelihood: -16362.419357
EM: Round [893] log likelihood: -16362.418707
EM: Round [894] log likelihood: -16362.418058
EM: Round [895] log likelihood: -16362.417410
EM: Round [896] log likelihood: -16362.416762
EM: Round [897] log likelihood: -16362.416115
EM: Round [898] log likelihood: -16362.415469
EM: Round [899] log likelihood: -16362.414825
EM: Round [900] log likelihood: -16362.414180
EM: Round [901] log likelihood: -16362.413537
EM: Round [902] log likelihood: -16362.412895
EM: Round [903] log likelihood: -16362.412253
EM: Round [904] log likelihood: -16362.411613
EM: Round [905] log likelihood: -16362.410973
EM: Round [906] log likelihood: -16362.410334
EM: Round [907] log likelihood: -16362.409696
EM: Round [908] log likelihood: -16362.409059
EM: Round [909] log likelihood: -16362.408422
EM: Round [910] log likelihood: -16362.407787
EM: Round [911] log likelihood: -16362.407152
EM: Round [912] log likelihood: -16362.406518
EM: Round [913] log likelihood: -16362.405885
EM: Round [914] log likelihood: -16362.405253
EM: Round [915] log likelihood: -16362.404622
EM: Round [916] log likelihood: -16362.403992
EM: Round [917] log likelihood: -16362.403362
EM: Round [918] log likelihood: -16362.402733
EM: Round [919] log likelihood: -16362.402105
EM: Round [920] log likelihood: -16362.401478
EM: Round [921] log likelihood: -16362.400852
EM: Round [922] log likelihood: -16362.400226
EM: Round [923] log likelihood: -16362.399602
EM: Round [924] log likelihood: -16362.398978
EM: Round [925] log likelihood: -16362.398355
EM: Round [926] log likelihood: -16362.397733
EM: Round [927] log likelihood: -16362.397111
EM: Round [928] log likelihood: -16362.396491
EM: Round [929] log likelihood: -16362.395871
EM: Round [930] log likelihood: -16362.395252
EM: Round [931] log likelihood: -16362.394634
EM: Round [932] log likelihood: -16362.394017
EM: Round [933] log likelihood: -16362.393401
EM: Round [934] log likelihood: -16362.392785
EM: Round [935] log likelihood: -16362.392170
EM: Round [936] log likelihood: -16362.391556
EM: Round [937] log likelihood: -16362.390943
EM: Round [938] log likelihood: -16362.390331
EM: Round [939] log likelihood: -16362.389719
EM: Round [940] log likelihood: -16362.389108
EM: Round [941] log likelihood: -16362.388498
EM: Round [942] log likelihood: -16362.387889
EM: Round [943] log likelihood: -16362.387281
EM: Round [944] log likelihood: -16362.386673
EM: Round [945] log likelihood: -16362.386066
EM: Round [946] log likelihood: -16362.385460
EM: Round [947] log likelihood: -16362.384855
EM: Round [948] log likelihood: -16362.384251
EM: Round [949] log likelihood: -16362.383647
EM: Round [950] log likelihood: -16362.383044
EM: Round [951] log likelihood: -16362.382442
EM: Round [952] log likelihood: -16362.381841
EM: Round [953] log likelihood: -16362.381240
EM: Round [954] log likelihood: -16362.380640
EM: Round [955] log likelihood: -16362.380041
EM: Round [956] log likelihood: -16362.379443
EM: Round [957] log likelihood: -16362.378846
EM: Round [958] log likelihood: -16362.378249
EM: Round [959] log likelihood: -16362.377653
EM: Round [960] log likelihood: -16362.377058
EM: Round [961] log likelihood: -16362.376464
EM: Round [962] log likelihood: -16362.375870
EM: Round [963] log likelihood: -16362.375278
EM: Round [964] log likelihood: -16362.374686
EM: Round [965] log likelihood: -16362.374094
EM: Round [966] log likelihood: -16362.373504
EM: Round [967] log likelihood: -16362.372914
EM: Round [968] log likelihood: -16362.372325
EM: Round [969] log likelihood: -16362.371737
EM: Round [970] log likelihood: -16362.371149
EM: Round [971] log likelihood: -16362.370563
EM: Round [972] log likelihood: -16362.369977
EM: Round [973] log likelihood: -16362.369392
EM: Round [974] log likelihood: -16362.368807
EM: Round [975] log likelihood: -16362.368224
EM: Round [976] log likelihood: -16362.367641
EM: Round [977] log likelihood: -16362.367058
EM: Round [978] log likelihood: -16362.366477
EM: Round [979] log likelihood: -16362.365896
EM: Round [980] log likelihood: -16362.365316
EM: Round [981] log likelihood: -16362.364737
EM: Round [982] log likelihood: -16362.364159
EM: Round [983] log likelihood: -16362.363581
EM: Round [984] log likelihood: -16362.363004
EM: Round [985] log likelihood: -16362.362427
EM: Round [986] log likelihood: -16362.361852
EM: Round [987] log likelihood: -16362.361277
EM: Round [988] log likelihood: -16362.360703
EM: Round [989] log likelihood: -16362.360130
EM: Round [990] log likelihood: -16362.359557
EM: Round [991] log likelihood: -16362.358985
EM: Round [992] log likelihood: -16362.358414
EM: Round [993] log likelihood: -16362.357844
EM: Round [994] log likelihood: -16362.357274
EM: Round [995] log likelihood: -16362.356705
EM: Round [996] log likelihood: -16362.356137
EM: Round [997] log likelihood: -16362.355569
EM: Round [998] log likelihood: -16362.355002
EM: Round [999] log likelihood: -16362.354436
EM: Round [1000] log likelihood: -16362.353871
EM: Round [1001] log likelihood: -16362.353306
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.12 minutes. CMD: samtools index /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 3.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir
-done, see /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -11068.564366
EM: Round [1] log likelihood: -11067.213459
EM: Round [2] log likelihood: -11067.135328
EM: Round [3] log likelihood: -11067.126607
EM: Round [4] log likelihood: -11067.121623
EM: Round [5] log likelihood: -11067.116862
EM: Round [6] log likelihood: -11067.112136
EM: Round [7] log likelihood: -11067.107437
EM: Round [8] log likelihood: -11067.102763
EM: Round [9] log likelihood: -11067.098115
EM: Round [10] log likelihood: -11067.093491
EM: Round [11] log likelihood: -11067.088891
EM: Round [12] log likelihood: -11067.084316
EM: Round [13] log likelihood: -11067.079764
EM: Round [14] log likelihood: -11067.075237
EM: Round [15] log likelihood: -11067.070733
EM: Round [16] log likelihood: -11067.066252
EM: Round [17] log likelihood: -11067.061794
EM: Round [18] log likelihood: -11067.057360
EM: Round [19] log likelihood: -11067.052948
EM: Round [20] log likelihood: -11067.048558
EM: Round [21] log likelihood: -11067.044191
EM: Round [22] log likelihood: -11067.039845
EM: Round [23] log likelihood: -11067.035522
EM: Round [24] log likelihood: -11067.031220
EM: Round [25] log likelihood: -11067.026939
EM: Round [26] log likelihood: -11067.022680
EM: Round [27] log likelihood: -11067.018442
EM: Round [28] log likelihood: -11067.014224
EM: Round [29] log likelihood: -11067.010028
EM: Round [30] log likelihood: -11067.005851
EM: Round [31] log likelihood: -11067.001695
EM: Round [32] log likelihood: -11066.997559
EM: Round [33] log likelihood: -11066.993443
EM: Round [34] log likelihood: -11066.989347
EM: Round [35] log likelihood: -11066.985270
EM: Round [36] log likelihood: -11066.981213
EM: Round [37] log likelihood: -11066.977175
EM: Round [38] log likelihood: -11066.973156
EM: Round [39] log likelihood: -11066.969155
EM: Round [40] log likelihood: -11066.965174
EM: Round [41] log likelihood: -11066.961211
EM: Round [42] log likelihood: -11066.957266
EM: Round [43] log likelihood: -11066.953340
EM: Round [44] log likelihood: -11066.949432
EM: Round [45] log likelihood: -11066.945542
EM: Round [46] log likelihood: -11066.941669
EM: Round [47] log likelihood: -11066.937814
EM: Round [48] log likelihood: -11066.933977
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EM: Round [964] log likelihood: -11065.655978
EM: Round [965] log likelihood: -11065.655416
EM: Round [966] log likelihood: -11065.654855
EM: Round [967] log likelihood: -11065.654295
EM: Round [968] log likelihood: -11065.653736
EM: Round [969] log likelihood: -11065.653177
EM: Round [970] log likelihood: -11065.652619
EM: Round [971] log likelihood: -11065.652061
EM: Round [972] log likelihood: -11065.651504
EM: Round [973] log likelihood: -11065.650948
EM: Round [974] log likelihood: -11065.650393
EM: Round [975] log likelihood: -11065.649838
EM: Round [976] log likelihood: -11065.649285
EM: Round [977] log likelihood: -11065.648731
EM: Round [978] log likelihood: -11065.648179
EM: Round [979] log likelihood: -11065.647627
EM: Round [980] log likelihood: -11065.647076
EM: Round [981] log likelihood: -11065.646525
EM: Round [982] log likelihood: -11065.645975
EM: Round [983] log likelihood: -11065.645426
EM: Round [984] log likelihood: -11065.644878
EM: Round [985] log likelihood: -11065.644330
EM: Round [986] log likelihood: -11065.643783
EM: Round [987] log likelihood: -11065.643237
EM: Round [988] log likelihood: -11065.642691
EM: Round [989] log likelihood: -11065.642146
EM: Round [990] log likelihood: -11065.641602
EM: Round [991] log likelihood: -11065.641058
EM: Round [992] log likelihood: -11065.640515
EM: Round [993] log likelihood: -11065.639973
EM: Round [994] log likelihood: -11065.639431
EM: Round [995] log likelihood: -11065.638890
EM: Round [996] log likelihood: -11065.638350
EM: Round [997] log likelihood: -11065.637810
EM: Round [998] log likelihood: -11065.637271
EM: Round [999] log likelihood: -11065.636733
EM: Round [1000] log likelihood: -11065.636196
EM: Round [1001] log likelihood: -11065.635659
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 282587251
Execution Time = 3.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.dkJEPjqjJR/fi_workdir/microH.dat
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.dkJEPjqjJR/fi_workdir/microH.dat /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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.dkJEPjqjJR/fi_workdir/microH.dat /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.dkJEPjqjJR --json_outfile /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.dkJEPjqjJR --json_outfile /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.dkJEPjqjJR/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.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000253778.1]
WARNING, no entry stored in dbm for [ENSG00000253778.1]
WARNING, no entry stored in dbm for [ENSG00000253778.1]
WARNING, no entry stored in dbm for [ENSG00000253778.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.dkJEPjqjJR/ctat_genome_lib_build_dir > /tmp/nxf.dkJEPjqjJR/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.dkJEPjqjJR/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory