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/e0/41a4413ff86c381a2c1fe39d3f8080/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/8d3634cd695171888017f8cc392a8f/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/dc427eb79239bd5125c1ca74fe1ba8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/dc427eb79239bd5125c1ca74fe1ba8/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/8d3634cd695171888017f8cc392a8f/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/cytoBand.txt
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.cqmxTZ3giy/fi_workdir --reads "/tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 08:24:07 ..... started STAR run
Jun 08 08:24:07 ..... loading genome
Jun 08 08:25:48 ... generating Suffix Array index
Jun 08 08:29:39 ... completed Suffix Array index
Jun 08 08:29:40 ..... processing annotations GTF
Jun 08 08:29:40 ..... inserting junctions into the genome indices
Jun 08 08:30:43 ..... started mapping
Jun 08 08:51:37 ..... finished mapping
Jun 08 08:51:38 ..... started sorting BAM
Jun 08 08:51:39 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 27.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.cqmxTZ3giy/fi_workdir --reads "/tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
08:51:42 : INFO : Done.
Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[530000] -done parsing /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 20,
' ** passed ** ' => 4863,
'exons hit < 2' => 7,
'excessive soft clipping' => 2980,
'seq-similar region overlap' => 60,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'per_id < 96' => 2623
};
-writing fusion junction support info.
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[70000] -fusion SPANNING read extraction for scaff: ARHGAP27--PKD1P6
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[1000] -fusion SPANNING read extraction for scaff: PPM1J--AL157944.1
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 16394,
'lacks exon overlap' => 6446
};
Execution Time = 0.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -1818.307133
EM: Round [1] log likelihood: -1818.013887
EM: Round [2] log likelihood: -1817.913627
EM: Round [3] log likelihood: -1817.831643
EM: Round [4] log likelihood: -1817.755042
EM: Round [5] log likelihood: -1817.682579
EM: Round [6] log likelihood: -1817.613870
EM: Round [7] log likelihood: -1817.548622
EM: Round [8] log likelihood: -1817.486577
EM: Round [9] log likelihood: -1817.427503
EM: Round [10] log likelihood: -1817.371191
EM: Round [11] log likelihood: -1817.317452
EM: Round [12] log likelihood: -1817.266112
EM: Round [13] log likelihood: -1817.217016
EM: Round [14] log likelihood: -1817.170021
EM: Round [15] log likelihood: -1817.124995
EM: Round [16] log likelihood: -1817.081818
EM: Round [17] log likelihood: -1817.040381
EM: Round [18] log likelihood: -1817.000580
EM: Round [19] log likelihood: -1816.962322
EM: Round [20] log likelihood: -1816.925520
EM: Round [21] log likelihood: -1816.890093
EM: Round [22] log likelihood: -1816.855967
EM: Round [23] log likelihood: -1816.823072
EM: Round [24] log likelihood: -1816.791343
EM: Round [25] log likelihood: -1816.760720
EM: Round [26] log likelihood: -1816.731147
EM: Round [27] log likelihood: -1816.702570
EM: Round [28] log likelihood: -1816.674941
EM: Round [29] log likelihood: -1816.648214
EM: Round [30] log likelihood: -1816.622344
EM: Round [31] log likelihood: -1816.597293
EM: Round [32] log likelihood: -1816.573020
EM: Round [33] log likelihood: -1816.549490
EM: Round [34] log likelihood: -1816.526671
EM: Round [35] log likelihood: -1816.504528
EM: Round [36] log likelihood: -1816.483034
EM: Round [37] log likelihood: -1816.462158
EM: Round [38] log likelihood: -1816.441875
EM: Round [39] log likelihood: -1816.422158
EM: Round [40] log likelihood: -1816.402985
EM: Round [41] log likelihood: -1816.384332
EM: Round [42] log likelihood: -1816.366177
EM: Round [43] log likelihood: -1816.348501
EM: Round [44] log likelihood: -1816.331285
EM: Round [45] log likelihood: -1816.314508
EM: Round [46] log likelihood: -1816.298156
EM: Round [47] log likelihood: -1816.282210
EM: Round [48] log likelihood: -1816.266655
EM: Round [49] log likelihood: -1816.251476
EM: Round [50] log likelihood: -1816.236659
EM: Round [51] log likelihood: -1816.222190
EM: Round [52] log likelihood: -1816.208057
EM: Round [53] log likelihood: -1816.194247
EM: Round [54] log likelihood: -1816.180748
EM: Round [55] log likelihood: -1816.167549
EM: Round [56] log likelihood: -1816.154640
EM: Round [57] log likelihood: -1816.142011
EM: Round [58] log likelihood: -1816.129651
EM: Round [59] log likelihood: -1816.117551
EM: Round [60] log likelihood: -1816.105703
EM: Round [61] log likelihood: -1816.094098
EM: Round [62] log likelihood: -1816.082729
EM: Round [63] log likelihood: -1816.071586
EM: Round [64] log likelihood: -1816.060663
EM: Round [65] log likelihood: -1816.049952
EM: Round [66] log likelihood: -1816.039448
EM: Round [67] log likelihood: -1816.029143
EM: Round [68] log likelihood: -1816.019031
EM: Round [69] log likelihood: -1816.009106
EM: Round [70] log likelihood: -1815.999362
EM: Round [71] log likelihood: -1815.989795
EM: Round [72] log likelihood: -1815.980398
EM: Round [73] log likelihood: -1815.971166
EM: Round [74] log likelihood: -1815.962095
EM: Round [75] log likelihood: -1815.953180
EM: Round [76] log likelihood: -1815.944417
EM: Round [77] log likelihood: -1815.935800
EM: Round [78] log likelihood: -1815.927327
EM: Round [79] log likelihood: -1815.918993
EM: Round [80] log likelihood: -1815.910793
EM: Round [81] log likelihood: -1815.902726
EM: Round [82] log likelihood: -1815.894786
EM: Round [83] log likelihood: -1815.886971
EM: Round [84] log likelihood: -1815.879277
EM: Round [85] log likelihood: -1815.871701
EM: Round [86] log likelihood: -1815.864240
EM: Round [87] log likelihood: -1815.856892
EM: Round [88] log likelihood: -1815.849652
EM: Round [89] log likelihood: -1815.842519
EM: Round [90] log likelihood: -1815.835490
EM: Round [91] log likelihood: -1815.828562
EM: Round [92] log likelihood: -1815.821733
EM: Round [93] log likelihood: -1815.815000
EM: Round [94] log likelihood: -1815.808362
EM: Round [95] log likelihood: -1815.801815
EM: Round [96] log likelihood: -1815.795358
EM: Round [97] log likelihood: -1815.788989
EM: Round [98] log likelihood: -1815.782706
EM: Round [99] log likelihood: -1815.776507
EM: Round [100] log likelihood: -1815.770390
EM: Round [101] log likelihood: -1815.764352
EM: Round [102] log likelihood: -1815.758394
EM: Round [103] log likelihood: -1815.752511
EM: Round [104] log likelihood: -1815.746704
EM: Round [105] log likelihood: -1815.740971
EM: Round [106] log likelihood: -1815.735309
EM: Round [107] log likelihood: -1815.729718
EM: Round [108] log likelihood: -1815.724196
EM: Round [109] log likelihood: -1815.718742
EM: Round [110] log likelihood: -1815.713354
EM: Round [111] log likelihood: -1815.708030
EM: Round [112] log likelihood: -1815.702771
EM: Round [113] log likelihood: -1815.697574
EM: Round [114] log likelihood: -1815.692438
EM: Round [115] log likelihood: -1815.687362
EM: Round [116] log likelihood: -1815.682345
EM: Round [117] log likelihood: -1815.677386
EM: Round [118] log likelihood: -1815.672484
EM: Round [119] log likelihood: -1815.667637
EM: Round [120] log likelihood: -1815.662845
EM: Round [121] log likelihood: -1815.658107
EM: Round [122] log likelihood: -1815.653422
EM: Round [123] log likelihood: -1815.648788
EM: Round [124] log likelihood: -1815.644206
EM: Round [125] log likelihood: -1815.639673
EM: Round [126] log likelihood: -1815.635190
EM: Round [127] log likelihood: -1815.630755
EM: Round [128] log likelihood: -1815.626367
EM: Round [129] log likelihood: -1815.622027
EM: Round [130] log likelihood: -1815.617732
EM: Round [131] log likelihood: -1815.613483
EM: Round [132] log likelihood: -1815.609278
EM: Round [133] log likelihood: -1815.605116
EM: Round [134] log likelihood: -1815.600998
EM: Round [135] log likelihood: -1815.596923
EM: Round [136] log likelihood: -1815.592889
EM: Round [137] log likelihood: -1815.588896
EM: Round [138] log likelihood: -1815.584943
EM: Round [139] log likelihood: -1815.581031
EM: Round [140] log likelihood: -1815.577157
EM: Round [141] log likelihood: -1815.573323
EM: Round [142] log likelihood: -1815.569526
EM: Round [143] log likelihood: -1815.565767
EM: Round [144] log likelihood: -1815.562044
EM: Round [145] log likelihood: -1815.558359
EM: Round [146] log likelihood: -1815.554709
EM: Round [147] log likelihood: -1815.551094
EM: Round [148] log likelihood: -1815.547514
EM: Round [149] log likelihood: -1815.543969
EM: Round [150] log likelihood: -1815.540458
EM: Round [151] log likelihood: -1815.536980
EM: Round [152] log likelihood: -1815.533535
EM: Round [153] log likelihood: -1815.530122
EM: Round [154] log likelihood: -1815.526742
EM: Round [155] log likelihood: -1815.523393
EM: Round [156] log likelihood: -1815.520075
EM: Round [157] log likelihood: -1815.516789
EM: Round [158] log likelihood: -1815.513532
EM: Round [159] log likelihood: -1815.510306
EM: Round [160] log likelihood: -1815.507109
EM: Round [161] log likelihood: -1815.503941
EM: Round [162] log likelihood: -1815.500802
EM: Round [163] log likelihood: -1815.497692
EM: Round [164] log likelihood: -1815.494610
EM: Round [165] log likelihood: -1815.491555
EM: Round [166] log likelihood: -1815.488528
EM: Round [167] log likelihood: -1815.485528
EM: Round [168] log likelihood: -1815.482555
EM: Round [169] log likelihood: -1815.479608
EM: Round [170] log likelihood: -1815.476687
EM: Round [171] log likelihood: -1815.473792
EM: Round [172] log likelihood: -1815.470922
EM: Round [173] log likelihood: -1815.468077
EM: Round [174] log likelihood: -1815.465258
EM: Round [175] log likelihood: -1815.462462
EM: Round [176] log likelihood: -1815.459691
EM: Round [177] log likelihood: -1815.456944
EM: Round [178] log likelihood: -1815.454221
EM: Round [179] log likelihood: -1815.451521
EM: Round [180] log likelihood: -1815.448844
EM: Round [181] log likelihood: -1815.446190
EM: Round [182] log likelihood: -1815.443559
EM: Round [183] log likelihood: -1815.440950
EM: Round [184] log likelihood: -1815.438363
EM: Round [185] log likelihood: -1815.435797
EM: Round [186] log likelihood: -1815.433254
EM: Round [187] log likelihood: -1815.430732
EM: Round [188] log likelihood: -1815.428230
EM: Round [189] log likelihood: -1815.425750
EM: Round [190] log likelihood: -1815.423291
EM: Round [191] log likelihood: -1815.420851
EM: Round [192] log likelihood: -1815.418432
EM: Round [193] log likelihood: -1815.416033
EM: Round [194] log likelihood: -1815.413654
EM: Round [195] log likelihood: -1815.411294
EM: Round [196] log likelihood: -1815.408954
EM: Round [197] log likelihood: -1815.406632
EM: Round [198] log likelihood: -1815.404330
EM: Round [199] log likelihood: -1815.402046
EM: Round [200] log likelihood: -1815.399781
EM: Round [201] log likelihood: -1815.397534
EM: Round [202] log likelihood: -1815.395306
EM: Round [203] log likelihood: -1815.393095
EM: Round [204] log likelihood: -1815.390902
EM: Round [205] log likelihood: -1815.388727
EM: Round [206] log likelihood: -1815.386569
EM: Round [207] log likelihood: -1815.384428
EM: Round [208] log likelihood: -1815.382304
EM: Round [209] log likelihood: -1815.380197
EM: Round [210] log likelihood: -1815.378107
EM: Round [211] log likelihood: -1815.376033
EM: Round [212] log likelihood: -1815.373976
EM: Round [213] log likelihood: -1815.371935
EM: Round [214] log likelihood: -1815.369910
EM: Round [215] log likelihood: -1815.367900
EM: Round [216] log likelihood: -1815.365907
EM: Round [217] log likelihood: -1815.363929
EM: Round [218] log likelihood: -1815.361966
EM: Round [219] log likelihood: -1815.360019
EM: Round [220] log likelihood: -1815.358087
EM: Round [221] log likelihood: -1815.356170
EM: Round [222] log likelihood: -1815.354267
EM: Round [223] log likelihood: -1815.352380
EM: Round [224] log likelihood: -1815.350506
EM: Round [225] log likelihood: -1815.348648
EM: Round [226] log likelihood: -1815.346803
EM: Round [227] log likelihood: -1815.344973
EM: Round [228] log likelihood: -1815.343156
EM: Round [229] log likelihood: -1815.341354
EM: Round [230] log likelihood: -1815.339565
EM: Round [231] log likelihood: -1815.337789
EM: Round [232] log likelihood: -1815.336028
EM: Round [233] log likelihood: -1815.334279
EM: Round [234] log likelihood: -1815.332544
EM: Round [235] log likelihood: -1815.330821
EM: Round [236] log likelihood: -1815.329112
EM: Round [237] log likelihood: -1815.327416
EM: Round [238] log likelihood: -1815.325732
EM: Round [239] log likelihood: -1815.324061
EM: Round [240] log likelihood: -1815.322402
EM: Round [241] log likelihood: -1815.320756
EM: Round [242] log likelihood: -1815.319122
EM: Round [243] log likelihood: -1815.317501
EM: Round [244] log likelihood: -1815.315891
EM: Round [245] log likelihood: -1815.314293
EM: Round [246] log likelihood: -1815.312707
EM: Round [247] log likelihood: -1815.311133
EM: Round [248] log likelihood: -1815.309570
EM: Round [249] log likelihood: -1815.308019
EM: Round [250] log likelihood: -1815.306479
EM: Round [251] log likelihood: -1815.304951
EM: Round [252] log likelihood: -1815.303434
EM: Round [253] log likelihood: -1815.301927
EM: Round [254] log likelihood: -1815.300432
EM: Round [255] log likelihood: -1815.298948
EM: Round [256] log likelihood: -1815.297475
EM: Round [257] log likelihood: -1815.296012
EM: Round [258] log likelihood: -1815.294560
EM: Round [259] log likelihood: -1815.293119
EM: Round [260] log likelihood: -1815.291687
EM: Round [261] log likelihood: -1815.290267
EM: Round [262] log likelihood: -1815.288856
EM: Round [263] log likelihood: -1815.287456
EM: Round [264] log likelihood: -1815.286066
EM: Round [265] log likelihood: -1815.284686
EM: Round [266] log likelihood: -1815.283315
EM: Round [267] log likelihood: -1815.281955
EM: Round [268] log likelihood: -1815.280604
EM: Round [269] log likelihood: -1815.279263
EM: Round [270] log likelihood: -1815.277932
EM: Round [271] log likelihood: -1815.276610
EM: Round [272] log likelihood: -1815.275297
EM: Round [273] log likelihood: -1815.273994
EM: Round [274] log likelihood: -1815.272700
EM: Round [275] log likelihood: -1815.271415
EM: Round [276] log likelihood: -1815.270140
EM: Round [277] log likelihood: -1815.268873
EM: Round [278] log likelihood: -1815.267616
EM: Round [279] log likelihood: -1815.266367
EM: Round [280] log likelihood: -1815.265127
EM: Round [281] log likelihood: -1815.263896
EM: Round [282] log likelihood: -1815.262673
EM: Round [283] log likelihood: -1815.261459
EM: Round [284] log likelihood: -1815.260254
EM: Round [285] log likelihood: -1815.259057
EM: Round [286] log likelihood: -1815.257868
EM: Round [287] log likelihood: -1815.256688
EM: Round [288] log likelihood: -1815.255515
EM: Round [289] log likelihood: -1815.254352
EM: Round [290] log likelihood: -1815.253196
EM: Round [291] log likelihood: -1815.252048
EM: Round [292] log likelihood: -1815.250908
EM: Round [293] log likelihood: -1815.249776
EM: Round [294] log likelihood: -1815.248652
EM: Round [295] log likelihood: -1815.247536
EM: Round [296] log likelihood: -1815.246428
EM: Round [297] log likelihood: -1815.245327
EM: Round [298] log likelihood: -1815.244234
EM: Round [299] log likelihood: -1815.243148
EM: Round [300] log likelihood: -1815.242070
EM: Round [301] log likelihood: -1815.240999
EM: Round [302] log likelihood: -1815.239935
EM: Round [303] log likelihood: -1815.238879
EM: Round [304] log likelihood: -1815.237830
EM: Round [305] log likelihood: -1815.236789
EM: Round [306] log likelihood: -1815.235754
EM: Round [307] log likelihood: -1815.234727
EM: Round [308] log likelihood: -1815.233706
EM: Round [309] log likelihood: -1815.232693
EM: Round [310] log likelihood: -1815.231686
EM: Round [311] log likelihood: -1815.230686
EM: Round [312] log likelihood: -1815.229693
EM: Round [313] log likelihood: -1815.228707
EM: Round [314] log likelihood: -1815.227728
EM: Round [315] log likelihood: -1815.226755
EM: Round [316] log likelihood: -1815.225789
EM: Round [317] log likelihood: -1815.224829
EM: Round [318] log likelihood: -1815.223876
EM: Round [319] log likelihood: -1815.222929
EM: Round [320] log likelihood: -1815.221989
EM: Round [321] log likelihood: -1815.221054
EM: Round [322] log likelihood: -1815.220127
EM: Round [323] log likelihood: -1815.219205
EM: Round [324] log likelihood: -1815.218290
EM: Round [325] log likelihood: -1815.217381
EM: Round [326] log likelihood: -1815.216478
EM: Round [327] log likelihood: -1815.215581
EM: Round [328] log likelihood: -1815.214690
EM: Round [329] log likelihood: -1815.213805
EM: Round [330] log likelihood: -1815.212926
EM: Round [331] log likelihood: -1815.212052
EM: Round [332] log likelihood: -1815.211185
EM: Round [333] log likelihood: -1815.210324
EM: Round [334] log likelihood: -1815.209468
EM: Round [335] log likelihood: -1815.208618
EM: Round [336] log likelihood: -1815.207773
EM: Round [337] log likelihood: -1815.206934
EM: Round [338] log likelihood: -1815.206101
EM: Round [339] log likelihood: -1815.205273
EM: Round [340] log likelihood: -1815.204451
EM: Round [341] log likelihood: -1815.203634
EM: Round [342] log likelihood: -1815.202823
EM: Round [343] log likelihood: -1815.202017
EM: Round [344] log likelihood: -1815.201216
EM: Round [345] log likelihood: -1815.200420
EM: Round [346] log likelihood: -1815.199630
EM: Round [347] log likelihood: -1815.198845
EM: Round [348] log likelihood: -1815.198066
EM: Round [349] log likelihood: -1815.197291
EM: Round [350] log likelihood: -1815.196521
EM: Round [351] log likelihood: -1815.195757
EM: Round [352] log likelihood: -1815.194997
EM: Round [353] log likelihood: -1815.194243
EM: Round [354] log likelihood: -1815.193493
EM: Round [355] log likelihood: -1815.192749
EM: Round [356] log likelihood: -1815.192009
EM: Round [357] log likelihood: -1815.191274
EM: Round [358] log likelihood: -1815.190544
EM: Round [359] log likelihood: -1815.189819
EM: Round [360] log likelihood: -1815.189098
EM: Round [361] log likelihood: -1815.188382
EM: Round [362] log likelihood: -1815.187671
EM: Round [363] log likelihood: -1815.186965
EM: Round [364] log likelihood: -1815.186263
EM: Round [365] log likelihood: -1815.185565
EM: Round [366] log likelihood: -1815.184872
EM: Round [367] log likelihood: -1815.184184
EM: Round [368] log likelihood: -1815.183500
EM: Round [369] log likelihood: -1815.182821
EM: Round [370] log likelihood: -1815.182146
EM: Round [371] log likelihood: -1815.181475
EM: Round [372] log likelihood: -1815.180809
EM: Round [373] log likelihood: -1815.180147
EM: Round [374] log likelihood: -1815.179489
EM: Round [375] log likelihood: -1815.178836
EM: Round [376] log likelihood: -1815.178186
EM: Round [377] log likelihood: -1815.177541
EM: Round [378] log likelihood: -1815.176900
EM: Round [379] log likelihood: -1815.176264
EM: Round [380] log likelihood: -1815.175631
EM: Round [381] log likelihood: -1815.175002
EM: Round [382] log likelihood: -1815.174378
EM: Round [383] log likelihood: -1815.173757
EM: Round [384] log likelihood: -1815.173141
EM: Round [385] log likelihood: -1815.172528
EM: Round [386] log likelihood: -1815.171920
EM: Round [387] log likelihood: -1815.171315
EM: Round [388] log likelihood: -1815.170714
EM: Round [389] log likelihood: -1815.170117
EM: Round [390] log likelihood: -1815.169524
EM: Round [391] log likelihood: -1815.168935
EM: Round [392] log likelihood: -1815.168349
EM: Round [393] log likelihood: -1815.167767
EM: Round [394] log likelihood: -1815.167189
EM: Round [395] log likelihood: -1815.166615
EM: Round [396] log likelihood: -1815.166044
EM: Round [397] log likelihood: -1815.165477
EM: Round [398] log likelihood: -1815.164913
EM: Round [399] log likelihood: -1815.164353
EM: Round [400] log likelihood: -1815.163797
EM: Round [401] log likelihood: -1815.163244
EM: Round [402] log likelihood: -1815.162695
EM: Round [403] log likelihood: -1815.162149
EM: Round [404] log likelihood: -1815.161607
EM: Round [405] log likelihood: -1815.161068
EM: Round [406] log likelihood: -1815.160532
EM: Round [407] log likelihood: -1815.160000
EM: Round [408] log likelihood: -1815.159471
EM: Round [409] log likelihood: -1815.158946
EM: Round [410] log likelihood: -1815.158424
EM: Round [411] log likelihood: -1815.157905
EM: Round [412] log likelihood: -1815.157390
EM: Round [413] log likelihood: -1815.156878
EM: Round [414] log likelihood: -1815.156369
EM: Round [415] log likelihood: -1815.155863
EM: Round [416] log likelihood: -1815.155360
EM: Round [417] log likelihood: -1815.154861
EM: Round [418] log likelihood: -1815.154365
EM: Round [419] log likelihood: -1815.153872
EM: Round [420] log likelihood: -1815.153382
EM: Round [421] log likelihood: -1815.152895
EM: Round [422] log likelihood: -1815.152411
EM: Round [423] log likelihood: -1815.151930
EM: Round [424] log likelihood: -1815.151453
EM: Round [425] log likelihood: -1815.150978
EM: Round [426] log likelihood: -1815.150506
EM: Round [427] log likelihood: -1815.150037
EM: Round [428] log likelihood: -1815.149571
EM: Round [429] log likelihood: -1815.149108
EM: Round [430] log likelihood: -1815.148648
EM: Round [431] log likelihood: -1815.148191
EM: Round [432] log likelihood: -1815.147737
EM: Round [433] log likelihood: -1815.147286
EM: Round [434] log likelihood: -1815.146837
EM: Round [435] log likelihood: -1815.146391
EM: Round [436] log likelihood: -1815.145948
EM: Round [437] log likelihood: -1815.145508
EM: Round [438] log likelihood: -1815.145070
EM: Round [439] log likelihood: -1815.144636
EM: Round [440] log likelihood: -1815.144204
EM: Round [441] log likelihood: -1815.143774
EM: Round [442] log likelihood: -1815.143348
EM: Round [443] log likelihood: -1815.142924
EM: Round [444] log likelihood: -1815.142502
EM: Round [445] log likelihood: -1815.142083
EM: Round [446] log likelihood: -1815.141667
EM: Round [447] log likelihood: -1815.141254
EM: Round [448] log likelihood: -1815.140843
EM: Round [449] log likelihood: -1815.140434
EM: Round [450] log likelihood: -1815.140029
EM: Round [451] log likelihood: -1815.139625
EM: Round [452] log likelihood: -1815.139224
EM: Round [453] log likelihood: -1815.138826
EM: Round [454] log likelihood: -1815.138430
EM: Round [455] log likelihood: -1815.138037
EM: Round [456] log likelihood: -1815.137646
EM: Round [457] log likelihood: -1815.137257
EM: Round [458] log likelihood: -1815.136871
EM: Round [459] log likelihood: -1815.136487
EM: Round [460] log likelihood: -1815.136106
EM: Round [461] log likelihood: -1815.135727
EM: Round [462] log likelihood: -1815.135350
EM: Round [463] log likelihood: -1815.134976
EM: Round [464] log likelihood: -1815.134604
EM: Round [465] log likelihood: -1815.134234
EM: Round [466] log likelihood: -1815.133867
EM: Round [467] log likelihood: -1815.133501
EM: Round [468] log likelihood: -1815.133139
EM: Round [469] log likelihood: -1815.132778
EM: Round [470] log likelihood: -1815.132419
EM: Round [471] log likelihood: -1815.132063
EM: Round [472] log likelihood: -1815.131709
EM: Round [473] log likelihood: -1815.131357
EM: Round [474] log likelihood: -1815.131008
EM: Round [475] log likelihood: -1815.130660
EM: Round [476] log likelihood: -1815.130315
EM: Round [477] log likelihood: -1815.129971
EM: Round [478] log likelihood: -1815.129630
EM: Round [479] log likelihood: -1815.129291
EM: Round [480] log likelihood: -1815.128954
EM: Round [481] log likelihood: -1815.128619
EM: Round [482] log likelihood: -1815.128287
EM: Round [483] log likelihood: -1815.127956
EM: Round [484] log likelihood: -1815.127627
EM: Round [485] log likelihood: -1815.127300
EM: Round [486] log likelihood: -1815.126975
EM: Round [487] log likelihood: -1815.126653
EM: Round [488] log likelihood: -1815.126332
EM: Round [489] log likelihood: -1815.126013
EM: Round [490] log likelihood: -1815.125696
EM: Round [491] log likelihood: -1815.125381
EM: Round [492] log likelihood: -1815.125068
EM: Round [493] log likelihood: -1815.124757
EM: Round [494] log likelihood: -1815.124448
EM: Round [495] log likelihood: -1815.124141
EM: Round [496] log likelihood: -1815.123836
EM: Round [497] log likelihood: -1815.123532
EM: Round [498] log likelihood: -1815.123230
EM: Round [499] log likelihood: -1815.122931
EM: Round [500] log likelihood: -1815.122633
EM: Round [501] log likelihood: -1815.122336
EM: Round [502] log likelihood: -1815.122042
EM: Round [503] log likelihood: -1815.121750
EM: Round [504] log likelihood: -1815.121459
EM: Round [505] log likelihood: -1815.121170
EM: Round [506] log likelihood: -1815.120883
EM: Round [507] log likelihood: -1815.120597
EM: Round [508] log likelihood: -1815.120313
EM: Round [509] log likelihood: -1815.120031
EM: Round [510] log likelihood: -1815.119751
EM: Round [511] log likelihood: -1815.119472
EM: Round [512] log likelihood: -1815.119196
EM: Round [513] log likelihood: -1815.118920
EM: Round [514] log likelihood: -1815.118647
EM: Round [515] log likelihood: -1815.118375
EM: Round [516] log likelihood: -1815.118105
EM: Round [517] log likelihood: -1815.117836
EM: Round [518] log likelihood: -1815.117569
EM: Round [519] log likelihood: -1815.117304
EM: Round [520] log likelihood: -1815.117040
EM: Round [521] log likelihood: -1815.116778
EM: Round [522] log likelihood: -1815.116518
EM: Round [523] log likelihood: -1815.116259
EM: Round [524] log likelihood: -1815.116001
EM: Round [525] log likelihood: -1815.115746
EM: Round [526] log likelihood: -1815.115491
EM: Round [527] log likelihood: -1815.115239
EM: Round [528] log likelihood: -1815.114987
EM: Round [529] log likelihood: -1815.114738
EM: Round [530] log likelihood: -1815.114490
EM: Round [531] log likelihood: -1815.114243
EM: Round [532] log likelihood: -1815.113998
EM: Round [533] log likelihood: -1815.113754
EM: Round [534] log likelihood: -1815.113512
EM: Round [535] log likelihood: -1815.113271
EM: Round [536] log likelihood: -1815.113032
EM: Round [537] log likelihood: -1815.112794
EM: Round [538] log likelihood: -1815.112558
EM: Round [539] log likelihood: -1815.112323
EM: Round [540] log likelihood: -1815.112090
EM: Round [541] log likelihood: -1815.111857
EM: Round [542] log likelihood: -1815.111627
EM: Round [543] log likelihood: -1815.111397
EM: Round [544] log likelihood: -1815.111170
EM: Round [545] log likelihood: -1815.110943
EM: Round [546] log likelihood: -1815.110718
EM: Round [547] log likelihood: -1815.110494
EM: Round [548] log likelihood: -1815.110272
EM: Round [549] log likelihood: -1815.110050
EM: Round [550] log likelihood: -1815.109831
EM: Round [551] log likelihood: -1815.109612
EM: Round [552] log likelihood: -1815.109395
EM: Round [553] log likelihood: -1815.109179
EM: Round [554] log likelihood: -1815.108965
EM: Round [555] log likelihood: -1815.108751
EM: Round [556] log likelihood: -1815.108539
EM: Round [557] log likelihood: -1815.108329
EM: Round [558] log likelihood: -1815.108119
EM: Round [559] log likelihood: -1815.107911
EM: Round [560] log likelihood: -1815.107704
EM: Round [561] log likelihood: -1815.107499
EM: Round [562] log likelihood: -1815.107294
EM: Round [563] log likelihood: -1815.107091
EM: Round [564] log likelihood: -1815.106889
EM: Round [565] log likelihood: -1815.106688
EM: Round [566] log likelihood: -1815.106489
EM: Round [567] log likelihood: -1815.106291
EM: Round [568] log likelihood: -1815.106093
EM: Round [569] log likelihood: -1815.105897
EM: Round [570] log likelihood: -1815.105703
EM: Round [571] log likelihood: -1815.105509
EM: Round [572] log likelihood: -1815.105317
EM: Round [573] log likelihood: -1815.105125
EM: Round [574] log likelihood: -1815.104935
EM: Round [575] log likelihood: -1815.104746
EM: Round [576] log likelihood: -1815.104558
EM: Round [577] log likelihood: -1815.104372
EM: Round [578] log likelihood: -1815.104186
EM: Round [579] log likelihood: -1815.104001
EM: Round [580] log likelihood: -1815.103818
EM: Round [581] log likelihood: -1815.103636
EM: Round [582] log likelihood: -1815.103454
EM: Round [583] log likelihood: -1815.103274
EM: Round [584] log likelihood: -1815.103095
EM: Round [585] log likelihood: -1815.102917
EM: Round [586] log likelihood: -1815.102740
EM: Round [587] log likelihood: -1815.102565
EM: Round [588] log likelihood: -1815.102390
EM: Round [589] log likelihood: -1815.102216
EM: Round [590] log likelihood: -1815.102043
EM: Round [591] log likelihood: -1815.101872
EM: Round [592] log likelihood: -1815.101701
EM: Round [593] log likelihood: -1815.101531
EM: Round [594] log likelihood: -1815.101363
EM: Round [595] log likelihood: -1815.101195
EM: Round [596] log likelihood: -1815.101029
EM: Round [597] log likelihood: -1815.100863
EM: Round [598] log likelihood: -1815.100698
EM: Round [599] log likelihood: -1815.100535
EM: Round [600] log likelihood: -1815.100372
EM: Round [601] log likelihood: -1815.100210
EM: Round [602] log likelihood: -1815.100050
EM: Round [603] log likelihood: -1815.099890
EM: Round [604] log likelihood: -1815.099731
EM: Round [605] log likelihood: -1815.099573
EM: Round [606] log likelihood: -1815.099416
EM: Round [607] log likelihood: -1815.099260
EM: Round [608] log likelihood: -1815.099105
EM: Round [609] log likelihood: -1815.098951
EM: Round [610] log likelihood: -1815.098798
EM: Round [611] log likelihood: -1815.098646
EM: Round [612] log likelihood: -1815.098494
EM: Round [613] log likelihood: -1815.098344
EM: Round [614] log likelihood: -1815.098194
EM: Round [615] log likelihood: -1815.098046
EM: Round [616] log likelihood: -1815.097898
EM: Round [617] log likelihood: -1815.097751
EM: Round [618] log likelihood: -1815.097605
EM: Round [619] log likelihood: -1815.097460
EM: Round [620] log likelihood: -1815.097315
EM: Round [621] log likelihood: -1815.097172
EM: Round [622] log likelihood: -1815.097029
EM: Round [623] log likelihood: -1815.096888
EM: Round [624] log likelihood: -1815.096747
EM: Round [625] log likelihood: -1815.096607
EM: Round [626] log likelihood: -1815.096467
EM: Round [627] log likelihood: -1815.096329
EM: Round [628] log likelihood: -1815.096191
EM: Round [629] log likelihood: -1815.096055
EM: Round [630] log likelihood: -1815.095919
EM: Round [631] log likelihood: -1815.095784
EM: Round [632] log likelihood: -1815.095649
EM: Round [633] log likelihood: -1815.095516
EM: Round [634] log likelihood: -1815.095383
EM: Round [635] log likelihood: -1815.095251
EM: Round [636] log likelihood: -1815.095120
EM: Round [637] log likelihood: -1815.094990
EM: Round [638] log likelihood: -1815.094860
EM: Round [639] log likelihood: -1815.094731
EM: Round [640] log likelihood: -1815.094603
EM: Round [641] log likelihood: -1815.094476
EM: Round [642] log likelihood: -1815.094349
EM: Round [643] log likelihood: -1815.094223
EM: Round [644] log likelihood: -1815.094098
EM: Round [645] log likelihood: -1815.093974
EM: Round [646] log likelihood: -1815.093850
EM: Round [647] log likelihood: -1815.093728
EM: Round [648] log likelihood: -1815.093605
EM: Round [649] log likelihood: -1815.093484
EM: Round [650] log likelihood: -1815.093363
EM: Round [651] log likelihood: -1815.093243
EM: Round [652] log likelihood: -1815.093124
EM: Round [653] log likelihood: -1815.093006
EM: Round [654] log likelihood: -1815.092888
EM: Round [655] log likelihood: -1815.092771
EM: Round [656] log likelihood: -1815.092654
EM: Round [657] log likelihood: -1815.092539
EM: Round [658] log likelihood: -1815.092423
EM: Round [659] log likelihood: -1815.092309
EM: Round [660] log likelihood: -1815.092195
EM: Round [661] log likelihood: -1815.092082
EM: Round [662] log likelihood: -1815.091970
EM: Round [663] log likelihood: -1815.091858
EM: Round [664] log likelihood: -1815.091747
EM: Round [665] log likelihood: -1815.091637
EM: Round [666] log likelihood: -1815.091527
EM: Round [667] log likelihood: -1815.091418
EM: Round [668] log likelihood: -1815.091310
EM: Round [669] log likelihood: -1815.091202
EM: Round [670] log likelihood: -1815.091095
EM: Round [671] log likelihood: -1815.090988
EM: Round [672] log likelihood: -1815.090882
EM: Round [673] log likelihood: -1815.090777
EM: Round [674] log likelihood: -1815.090673
EM: Round [675] log likelihood: -1815.090569
EM: Round [676] log likelihood: -1815.090465
EM: Round [677] log likelihood: -1815.090362
EM: Round [678] log likelihood: -1815.090260
EM: Round [679] log likelihood: -1815.090159
EM: Round [680] log likelihood: -1815.090058
EM: Round [681] log likelihood: -1815.089957
EM: Round [682] log likelihood: -1815.089857
EM: Stopping iterations at round 682 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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir
-done, see /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1227.026214
EM: Round [1] log likelihood: -1226.824098
EM: Round [2] log likelihood: -1226.809651
EM: Round [3] log likelihood: -1226.808633
EM: Round [4] log likelihood: -1226.808561
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 105119483
Execution Time = 2.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/fi_workdir/microH.dat
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.cqmxTZ3giy/fi_workdir/microH.dat /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/microH.dat /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.cqmxTZ3giy --json_outfile /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_PCB_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.cqmxTZ3giy --json_outfile /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory