Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/07ceeaac91efe0f36bd706b1dc276f/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e0d4fca38a8cbb7592bbf3a31f4d8e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e0d4fca38a8cbb7592bbf3a31f4d8e/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b69d105f2c4c3bbd740585d6987707/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b69d105f2c4c3bbd740585d6987707/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/cytoBand.txt
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.tExeCh6s5b/fi_workdir --reads "/tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:28:52 ..... started STAR run
Jun 08 09:28:52 ..... loading genome
Jun 08 09:30:36 ... generating Suffix Array index
Jun 08 09:34:22 ... completed Suffix Array index
Jun 08 09:34:22 ..... processing annotations GTF
Jun 08 09:34:22 ..... inserting junctions into the genome indices
Jun 08 09:35:23 ..... started mapping
Jun 08 10:28:49 ..... finished mapping
Jun 08 10:28:51 ..... started sorting BAM
Jun 08 10:28:53 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 60.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.tExeCh6s5b/fi_workdir --reads "/tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:29:13 : INFO : Done.
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3130000] -done parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 8538,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4774,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'exons hit < 2' => 9,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
' ** passed ** ' => 86732,
'low complexity anchor region' => 164,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 48,
'excessive soft clipping' => 14574,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
'small anchor length' => 1032,
'num genes matched < 2' => 675,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 439,
'seq-similar region overlap' => 1950
};
-writing fusion junction support info.
Execution Time = 1.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[1119000] -fusion SPANNING read extraction for scaff: NAB2--STAT6
[1000]
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[30000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1
[1000]
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[32000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2
[1000]
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[45000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHA13
[1000]
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[34000]
[35000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
[1000]
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
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[35000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[76000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[69000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[33000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[1109000] -fusion SPANNING read extraction for scaff: STAT6--NAB2
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[55000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[33000] -fusion SPANNING read extraction for scaff: TMEM14B--FER1L5
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[49000] -fusion SPANNING read extraction for scaff: XACT--LRRTM4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 40031,
'lacks exon overlap' => 83379
};
Execution Time = 5.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -28022.081655
EM: Round [1] log likelihood: -27862.529170
EM: Round [2] log likelihood: -27842.984221
EM: Round [3] log likelihood: -27829.961751
EM: Round [4] log likelihood: -27820.699505
EM: Round [5] log likelihood: -27814.022304
EM: Round [6] log likelihood: -27809.140933
EM: Round [7] log likelihood: -27805.515813
EM: Round [8] log likelihood: -27802.774392
EM: Round [9] log likelihood: -27800.657620
EM: Round [10] log likelihood: -27798.984458
EM: Round [11] log likelihood: -27797.627941
EM: Round [12] log likelihood: -27796.498800
EM: Round [13] log likelihood: -27795.534148
EM: Round [14] log likelihood: -27794.689605
EM: Round [15] log likelihood: -27793.933803
EM: Round [16] log likelihood: -27793.244525
EM: Round [17] log likelihood: -27792.605998
EM: Round [18] log likelihood: -27792.006989
EM: Round [19] log likelihood: -27791.439463
EM: Round [20] log likelihood: -27790.897641
EM: Round [21] log likelihood: -27790.377340
EM: Round [22] log likelihood: -27789.875498
EM: Round [23] log likelihood: -27789.389852
EM: Round [24] log likelihood: -27788.918703
EM: Round [25] log likelihood: -27788.460752
EM: Round [26] log likelihood: -27788.014989
EM: Round [27] log likelihood: -27787.580607
EM: Round [28] log likelihood: -27787.156950
EM: Round [29] log likelihood: -27786.743467
EM: Round [30] log likelihood: -27786.339687
EM: Round [31] log likelihood: -27785.945199
EM: Round [32] log likelihood: -27785.559636
EM: Round [33] log likelihood: -27785.182666
EM: Round [34] log likelihood: -27784.813981
EM: Round [35] log likelihood: -27784.453300
EM: Round [36] log likelihood: -27784.100354
EM: Round [37] log likelihood: -27783.754892
EM: Round [38] log likelihood: -27783.416677
EM: Round [39] log likelihood: -27783.085480
EM: Round [40] log likelihood: -27782.761084
EM: Round [41] log likelihood: -27782.443282
EM: Round [42] log likelihood: -27782.131874
EM: Round [43] log likelihood: -27781.826668
EM: Round [44] log likelihood: -27781.527480
EM: Round [45] log likelihood: -27781.234131
EM: Round [46] log likelihood: -27780.946453
EM: Round [47] log likelihood: -27780.664279
EM: Round [48] log likelihood: -27780.387451
EM: Round [49] log likelihood: -27780.115816
EM: Round [50] log likelihood: -27779.849226
EM: Round [51] log likelihood: -27779.587540
EM: Round [52] log likelihood: -27779.330620
EM: Round [53] log likelihood: -27779.078334
EM: Round [54] log likelihood: -27778.830554
EM: Round [55] log likelihood: -27778.587157
EM: Round [56] log likelihood: -27778.348023
EM: Round [57] log likelihood: -27778.113039
EM: Round [58] log likelihood: -27777.882093
EM: Round [59] log likelihood: -27777.655079
EM: Round [60] log likelihood: -27777.431893
EM: Round [61] log likelihood: -27777.212435
EM: Round [62] log likelihood: -27776.996610
EM: Round [63] log likelihood: -27776.784324
EM: Round [64] log likelihood: -27776.575488
EM: Round [65] log likelihood: -27776.370015
EM: Round [66] log likelihood: -27776.167821
EM: Round [67] log likelihood: -27775.968825
EM: Round [68] log likelihood: -27775.772948
EM: Round [69] log likelihood: -27775.580116
EM: Round [70] log likelihood: -27775.390255
EM: Round [71] log likelihood: -27775.203294
EM: Round [72] log likelihood: -27775.019164
EM: Round [73] log likelihood: -27774.837801
EM: Round [74] log likelihood: -27774.659139
EM: Round [75] log likelihood: -27774.483117
EM: Round [76] log likelihood: -27774.309674
EM: Round [77] log likelihood: -27774.138753
EM: Round [78] log likelihood: -27773.970297
EM: Round [79] log likelihood: -27773.804252
EM: Round [80] log likelihood: -27773.640566
EM: Round [81] log likelihood: -27773.479186
EM: Round [82] log likelihood: -27773.320064
EM: Round [83] log likelihood: -27773.163151
EM: Round [84] log likelihood: -27773.008401
EM: Round [85] log likelihood: -27772.855768
EM: Round [86] log likelihood: -27772.705210
EM: Round [87] log likelihood: -27772.556682
EM: Round [88] log likelihood: -27772.410145
EM: Round [89] log likelihood: -27772.265558
EM: Round [90] log likelihood: -27772.122881
EM: Round [91] log likelihood: -27771.982078
EM: Round [92] log likelihood: -27771.843112
EM: Round [93] log likelihood: -27771.705946
EM: Round [94] log likelihood: -27771.570546
EM: Round [95] log likelihood: -27771.436879
EM: Round [96] log likelihood: -27771.304911
EM: Round [97] log likelihood: -27771.174611
EM: Round [98] log likelihood: -27771.045947
EM: Round [99] log likelihood: -27770.918890
EM: Round [100] log likelihood: -27770.793411
EM: Round [101] log likelihood: -27770.669479
EM: Round [102] log likelihood: -27770.547069
EM: Round [103] log likelihood: -27770.426151
EM: Round [104] log likelihood: -27770.306701
EM: Round [105] log likelihood: -27770.188692
EM: Round [106] log likelihood: -27770.072099
EM: Round [107] log likelihood: -27769.956897
EM: Round [108] log likelihood: -27769.843063
EM: Round [109] log likelihood: -27769.730574
EM: Round [110] log likelihood: -27769.619406
EM: Round [111] log likelihood: -27769.509538
EM: Round [112] log likelihood: -27769.400948
EM: Round [113] log likelihood: -27769.293614
EM: Round [114] log likelihood: -27769.187516
EM: Round [115] log likelihood: -27769.082635
EM: Round [116] log likelihood: -27768.978949
EM: Round [117] log likelihood: -27768.876441
EM: Round [118] log likelihood: -27768.775091
EM: Round [119] log likelihood: -27768.674881
EM: Round [120] log likelihood: -27768.575792
EM: Round [121] log likelihood: -27768.477808
EM: Round [122] log likelihood: -27768.380912
EM: Round [123] log likelihood: -27768.285086
EM: Round [124] log likelihood: -27768.190313
EM: Round [125] log likelihood: -27768.096579
EM: Round [126] log likelihood: -27768.003867
EM: Round [127] log likelihood: -27767.912162
EM: Round [128] log likelihood: -27767.821449
EM: Round [129] log likelihood: -27767.731712
EM: Round [130] log likelihood: -27767.642938
EM: Round [131] log likelihood: -27767.555113
EM: Round [132] log likelihood: -27767.468223
EM: Round [133] log likelihood: -27767.382253
EM: Round [134] log likelihood: -27767.297191
EM: Round [135] log likelihood: -27767.213024
EM: Round [136] log likelihood: -27767.129739
EM: Round [137] log likelihood: -27767.047323
EM: Round [138] log likelihood: -27766.965765
EM: Round [139] log likelihood: -27766.885051
EM: Round [140] log likelihood: -27766.805171
EM: Round [141] log likelihood: -27766.726113
EM: Round [142] log likelihood: -27766.647865
EM: Round [143] log likelihood: -27766.570416
EM: Round [144] log likelihood: -27766.493756
EM: Round [145] log likelihood: -27766.417873
EM: Round [146] log likelihood: -27766.342758
EM: Round [147] log likelihood: -27766.268399
EM: Round [148] log likelihood: -27766.194787
EM: Round [149] log likelihood: -27766.121911
EM: Round [150] log likelihood: -27766.049763
EM: Round [151] log likelihood: -27765.978332
EM: Round [152] log likelihood: -27765.907608
EM: Round [153] log likelihood: -27765.837583
EM: Round [154] log likelihood: -27765.768248
EM: Round [155] log likelihood: -27765.699594
EM: Round [156] log likelihood: -27765.631611
EM: Round [157] log likelihood: -27765.564292
EM: Round [158] log likelihood: -27765.497627
EM: Round [159] log likelihood: -27765.431608
EM: Round [160] log likelihood: -27765.366228
EM: Round [161] log likelihood: -27765.301478
EM: Round [162] log likelihood: -27765.237351
EM: Round [163] log likelihood: -27765.173837
EM: Round [164] log likelihood: -27765.110931
EM: Round [165] log likelihood: -27765.048624
EM: Round [166] log likelihood: -27764.986909
EM: Round [167] log likelihood: -27764.925778
EM: Round [168] log likelihood: -27764.865225
EM: Round [169] log likelihood: -27764.805242
EM: Round [170] log likelihood: -27764.745823
EM: Round [171] log likelihood: -27764.686961
EM: Round [172] log likelihood: -27764.628649
EM: Round [173] log likelihood: -27764.570880
EM: Round [174] log likelihood: -27764.513648
EM: Round [175] log likelihood: -27764.456946
EM: Round [176] log likelihood: -27764.400769
EM: Round [177] log likelihood: -27764.345110
EM: Round [178] log likelihood: -27764.289962
EM: Round [179] log likelihood: -27764.235321
EM: Round [180] log likelihood: -27764.181179
EM: Round [181] log likelihood: -27764.127532
EM: Round [182] log likelihood: -27764.074374
EM: Round [183] log likelihood: -27764.021698
EM: Round [184] log likelihood: -27763.969499
EM: Round [185] log likelihood: -27763.917773
EM: Round [186] log likelihood: -27763.866512
EM: Round [187] log likelihood: -27763.815713
EM: Round [188] log likelihood: -27763.765370
EM: Round [189] log likelihood: -27763.715477
EM: Round [190] log likelihood: -27763.666031
EM: Round [191] log likelihood: -27763.617024
EM: Round [192] log likelihood: -27763.568454
EM: Round [193] log likelihood: -27763.520314
EM: Round [194] log likelihood: -27763.472601
EM: Round [195] log likelihood: -27763.425308
EM: Round [196] log likelihood: -27763.378433
EM: Round [197] log likelihood: -27763.331969
EM: Round [198] log likelihood: -27763.285914
EM: Round [199] log likelihood: -27763.240261
EM: Round [200] log likelihood: -27763.195007
EM: Round [201] log likelihood: -27763.150147
EM: Round [202] log likelihood: -27763.105678
EM: Round [203] log likelihood: -27763.061595
EM: Round [204] log likelihood: -27763.017893
EM: Round [205] log likelihood: -27762.974569
EM: Round [206] log likelihood: -27762.931619
EM: Round [207] log likelihood: -27762.889038
EM: Round [208] log likelihood: -27762.846823
EM: Round [209] log likelihood: -27762.804970
EM: Round [210] log likelihood: -27762.763475
EM: Round [211] log likelihood: -27762.722334
EM: Round [212] log likelihood: -27762.681544
EM: Round [213] log likelihood: -27762.641100
EM: Round [214] log likelihood: -27762.601000
EM: Round [215] log likelihood: -27762.561240
EM: Round [216] log likelihood: -27762.521816
EM: Round [217] log likelihood: -27762.482724
EM: Round [218] log likelihood: -27762.443961
EM: Round [219] log likelihood: -27762.405525
EM: Round [220] log likelihood: -27762.367411
EM: Round [221] log likelihood: -27762.329616
EM: Round [222] log likelihood: -27762.292137
EM: Round [223] log likelihood: -27762.254971
EM: Round [224] log likelihood: -27762.218114
EM: Round [225] log likelihood: -27762.181564
EM: Round [226] log likelihood: -27762.145317
EM: Round [227] log likelihood: -27762.109371
EM: Round [228] log likelihood: -27762.073721
EM: Round [229] log likelihood: -27762.038366
EM: Round [230] log likelihood: -27762.003302
EM: Round [231] log likelihood: -27761.968527
EM: Round [232] log likelihood: -27761.934037
EM: Round [233] log likelihood: -27761.899830
EM: Round [234] log likelihood: -27761.865903
EM: Round [235] log likelihood: -27761.832253
EM: Round [236] log likelihood: -27761.798878
EM: Round [237] log likelihood: -27761.765774
EM: Round [238] log likelihood: -27761.732940
EM: Round [239] log likelihood: -27761.700372
EM: Round [240] log likelihood: -27761.668068
EM: Round [241] log likelihood: -27761.636025
EM: Round [242] log likelihood: -27761.604241
EM: Round [243] log likelihood: -27761.572713
EM: Round [244] log likelihood: -27761.541439
EM: Round [245] log likelihood: -27761.510416
EM: Round [246] log likelihood: -27761.479643
EM: Round [247] log likelihood: -27761.449116
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EM: Round [707] log likelihood: -27757.397794
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EM: Round [709] log likelihood: -27757.395085
EM: Round [710] log likelihood: -27757.393743
EM: Round [711] log likelihood: -27757.392410
EM: Round [712] log likelihood: -27757.391084
EM: Round [713] log likelihood: -27757.389767
EM: Round [714] log likelihood: -27757.388458
EM: Round [715] log likelihood: -27757.387157
EM: Round [716] log likelihood: -27757.385864
EM: Round [717] log likelihood: -27757.384579
EM: Round [718] log likelihood: -27757.383303
EM: Round [719] log likelihood: -27757.382034
EM: Round [720] log likelihood: -27757.380772
EM: Round [721] log likelihood: -27757.379519
EM: Round [722] log likelihood: -27757.378273
EM: Round [723] log likelihood: -27757.377035
EM: Round [724] log likelihood: -27757.375805
EM: Round [725] log likelihood: -27757.374582
EM: Round [726] log likelihood: -27757.373367
EM: Round [727] log likelihood: -27757.372160
EM: Round [728] log likelihood: -27757.370959
EM: Round [729] log likelihood: -27757.369767
EM: Round [730] log likelihood: -27757.368581
EM: Round [731] log likelihood: -27757.367403
EM: Round [732] log likelihood: -27757.366232
EM: Round [733] log likelihood: -27757.365069
EM: Round [734] log likelihood: -27757.363912
EM: Round [735] log likelihood: -27757.362763
EM: Round [736] log likelihood: -27757.361621
EM: Round [737] log likelihood: -27757.360486
EM: Round [738] log likelihood: -27757.359358
EM: Round [739] log likelihood: -27757.358236
EM: Round [740] log likelihood: -27757.357122
EM: Round [741] log likelihood: -27757.356015
EM: Round [742] log likelihood: -27757.354914
EM: Round [743] log likelihood: -27757.353820
EM: Round [744] log likelihood: -27757.352733
EM: Round [745] log likelihood: -27757.351653
EM: Round [746] log likelihood: -27757.350579
EM: Round [747] log likelihood: -27757.349512
EM: Round [748] log likelihood: -27757.348452
EM: Round [749] log likelihood: -27757.347398
EM: Round [750] log likelihood: -27757.346350
EM: Round [751] log likelihood: -27757.345309
EM: Round [752] log likelihood: -27757.344274
EM: Round [753] log likelihood: -27757.343246
EM: Round [754] log likelihood: -27757.342224
EM: Round [755] log likelihood: -27757.341209
EM: Round [756] log likelihood: -27757.340199
EM: Round [757] log likelihood: -27757.339196
EM: Round [758] log likelihood: -27757.338199
EM: Round [759] log likelihood: -27757.337208
EM: Round [760] log likelihood: -27757.336223
EM: Round [761] log likelihood: -27757.335245
EM: Round [762] log likelihood: -27757.334272
EM: Round [763] log likelihood: -27757.333305
EM: Round [764] log likelihood: -27757.332344
EM: Round [765] log likelihood: -27757.331390
EM: Round [766] log likelihood: -27757.330441
EM: Round [767] log likelihood: -27757.329497
EM: Round [768] log likelihood: -27757.328560
EM: Round [769] log likelihood: -27757.327628
EM: Round [770] log likelihood: -27757.326702
EM: Round [771] log likelihood: -27757.325782
EM: Round [772] log likelihood: -27757.324868
EM: Round [773] log likelihood: -27757.323959
EM: Round [774] log likelihood: -27757.323056
EM: Round [775] log likelihood: -27757.322158
EM: Round [776] log likelihood: -27757.321265
EM: Round [777] log likelihood: -27757.320379
EM: Round [778] log likelihood: -27757.319497
EM: Round [779] log likelihood: -27757.318621
EM: Round [780] log likelihood: -27757.317751
EM: Round [781] log likelihood: -27757.316886
EM: Round [782] log likelihood: -27757.316026
EM: Round [783] log likelihood: -27757.315171
EM: Round [784] log likelihood: -27757.314322
EM: Round [785] log likelihood: -27757.313478
EM: Round [786] log likelihood: -27757.312639
EM: Round [787] log likelihood: -27757.311805
EM: Round [788] log likelihood: -27757.310976
EM: Round [789] log likelihood: -27757.310152
EM: Round [790] log likelihood: -27757.309334
EM: Round [791] log likelihood: -27757.308520
EM: Round [792] log likelihood: -27757.307712
EM: Round [793] log likelihood: -27757.306908
EM: Round [794] log likelihood: -27757.306109
EM: Round [795] log likelihood: -27757.305316
EM: Round [796] log likelihood: -27757.304527
EM: Round [797] log likelihood: -27757.303743
EM: Round [798] log likelihood: -27757.302963
EM: Round [799] log likelihood: -27757.302189
EM: Round [800] log likelihood: -27757.301419
EM: Round [801] log likelihood: -27757.300654
EM: Round [802] log likelihood: -27757.299894
EM: Round [803] log likelihood: -27757.299138
EM: Round [804] log likelihood: -27757.298387
EM: Round [805] log likelihood: -27757.297640
EM: Round [806] log likelihood: -27757.296899
EM: Round [807] log likelihood: -27757.296161
EM: Round [808] log likelihood: -27757.295428
EM: Round [809] log likelihood: -27757.294700
EM: Round [810] log likelihood: -27757.293976
EM: Round [811] log likelihood: -27757.293257
EM: Round [812] log likelihood: -27757.292542
EM: Round [813] log likelihood: -27757.291831
EM: Round [814] log likelihood: -27757.291125
EM: Round [815] log likelihood: -27757.290423
EM: Round [816] log likelihood: -27757.289725
EM: Round [817] log likelihood: -27757.289032
EM: Round [818] log likelihood: -27757.288342
EM: Round [819] log likelihood: -27757.287657
EM: Round [820] log likelihood: -27757.286977
EM: Round [821] log likelihood: -27757.286300
EM: Round [822] log likelihood: -27757.285628
EM: Round [823] log likelihood: -27757.284959
EM: Round [824] log likelihood: -27757.284295
EM: Round [825] log likelihood: -27757.283635
EM: Round [826] log likelihood: -27757.282979
EM: Round [827] log likelihood: -27757.282326
EM: Round [828] log likelihood: -27757.281678
EM: Round [829] log likelihood: -27757.281034
EM: Round [830] log likelihood: -27757.280394
EM: Round [831] log likelihood: -27757.279757
EM: Round [832] log likelihood: -27757.279125
EM: Round [833] log likelihood: -27757.278496
EM: Round [834] log likelihood: -27757.277872
EM: Round [835] log likelihood: -27757.277251
EM: Round [836] log likelihood: -27757.276634
EM: Round [837] log likelihood: -27757.276020
EM: Round [838] log likelihood: -27757.275411
EM: Round [839] log likelihood: -27757.274805
EM: Round [840] log likelihood: -27757.274202
EM: Round [841] log likelihood: -27757.273604
EM: Round [842] log likelihood: -27757.273009
EM: Round [843] log likelihood: -27757.272418
EM: Round [844] log likelihood: -27757.271830
EM: Round [845] log likelihood: -27757.271246
EM: Round [846] log likelihood: -27757.270666
EM: Round [847] log likelihood: -27757.270089
EM: Round [848] log likelihood: -27757.269515
EM: Round [849] log likelihood: -27757.268946
EM: Round [850] log likelihood: -27757.268379
EM: Round [851] log likelihood: -27757.267816
EM: Round [852] log likelihood: -27757.267257
EM: Round [853] log likelihood: -27757.266701
EM: Round [854] log likelihood: -27757.266148
EM: Round [855] log likelihood: -27757.265599
EM: Round [856] log likelihood: -27757.265053
EM: Round [857] log likelihood: -27757.264510
EM: Round [858] log likelihood: -27757.263971
EM: Round [859] log likelihood: -27757.263435
EM: Round [860] log likelihood: -27757.262902
EM: Round [861] log likelihood: -27757.262372
EM: Round [862] log likelihood: -27757.261846
EM: Round [863] log likelihood: -27757.261323
EM: Round [864] log likelihood: -27757.260803
EM: Round [865] log likelihood: -27757.260286
EM: Round [866] log likelihood: -27757.259773
EM: Round [867] log likelihood: -27757.259262
EM: Round [868] log likelihood: -27757.258755
EM: Round [869] log likelihood: -27757.258251
EM: Round [870] log likelihood: -27757.257750
EM: Round [871] log likelihood: -27757.257251
EM: Round [872] log likelihood: -27757.256756
EM: Round [873] log likelihood: -27757.256264
EM: Round [874] log likelihood: -27757.255775
EM: Round [875] log likelihood: -27757.255289
EM: Round [876] log likelihood: -27757.254806
EM: Round [877] log likelihood: -27757.254326
EM: Round [878] log likelihood: -27757.253849
EM: Round [879] log likelihood: -27757.253374
EM: Round [880] log likelihood: -27757.252903
EM: Round [881] log likelihood: -27757.252434
EM: Round [882] log likelihood: -27757.251969
EM: Round [883] log likelihood: -27757.251506
EM: Round [884] log likelihood: -27757.251046
EM: Round [885] log likelihood: -27757.250589
EM: Round [886] log likelihood: -27757.250134
EM: Round [887] log likelihood: -27757.249682
EM: Round [888] log likelihood: -27757.249233
EM: Round [889] log likelihood: -27757.248787
EM: Round [890] log likelihood: -27757.248344
EM: Round [891] log likelihood: -27757.247903
EM: Round [892] log likelihood: -27757.247465
EM: Round [893] log likelihood: -27757.247029
EM: Round [894] log likelihood: -27757.246597
EM: Round [895] log likelihood: -27757.246167
EM: Round [896] log likelihood: -27757.245739
EM: Round [897] log likelihood: -27757.245314
EM: Round [898] log likelihood: -27757.244892
EM: Round [899] log likelihood: -27757.244472
EM: Round [900] log likelihood: -27757.244055
EM: Round [901] log likelihood: -27757.243640
EM: Round [902] log likelihood: -27757.243228
EM: Round [903] log likelihood: -27757.242818
EM: Round [904] log likelihood: -27757.242411
EM: Round [905] log likelihood: -27757.242006
EM: Round [906] log likelihood: -27757.241604
EM: Round [907] log likelihood: -27757.241205
EM: Round [908] log likelihood: -27757.240807
EM: Round [909] log likelihood: -27757.240412
EM: Round [910] log likelihood: -27757.240020
EM: Round [911] log likelihood: -27757.239630
EM: Round [912] log likelihood: -27757.239242
EM: Round [913] log likelihood: -27757.238857
EM: Round [914] log likelihood: -27757.238473
EM: Round [915] log likelihood: -27757.238093
EM: Round [916] log likelihood: -27757.237714
EM: Round [917] log likelihood: -27757.237338
EM: Round [918] log likelihood: -27757.236964
EM: Round [919] log likelihood: -27757.236593
EM: Round [920] log likelihood: -27757.236224
EM: Round [921] log likelihood: -27757.235857
EM: Round [922] log likelihood: -27757.235492
EM: Round [923] log likelihood: -27757.235129
EM: Round [924] log likelihood: -27757.234769
EM: Round [925] log likelihood: -27757.234411
EM: Round [926] log likelihood: -27757.234055
EM: Round [927] log likelihood: -27757.233701
EM: Round [928] log likelihood: -27757.233349
EM: Round [929] log likelihood: -27757.233000
EM: Round [930] log likelihood: -27757.232652
EM: Round [931] log likelihood: -27757.232307
EM: Round [932] log likelihood: -27757.231964
EM: Round [933] log likelihood: -27757.231622
EM: Round [934] log likelihood: -27757.231283
EM: Round [935] log likelihood: -27757.230946
EM: Round [936] log likelihood: -27757.230611
EM: Round [937] log likelihood: -27757.230279
EM: Round [938] log likelihood: -27757.229948
EM: Round [939] log likelihood: -27757.229619
EM: Round [940] log likelihood: -27757.229292
EM: Round [941] log likelihood: -27757.228967
EM: Round [942] log likelihood: -27757.228644
EM: Round [943] log likelihood: -27757.228323
EM: Round [944] log likelihood: -27757.228004
EM: Round [945] log likelihood: -27757.227687
EM: Round [946] log likelihood: -27757.227372
EM: Round [947] log likelihood: -27757.227059
EM: Round [948] log likelihood: -27757.226747
EM: Round [949] log likelihood: -27757.226438
EM: Round [950] log likelihood: -27757.226130
EM: Round [951] log likelihood: -27757.225825
EM: Round [952] log likelihood: -27757.225521
EM: Round [953] log likelihood: -27757.225219
EM: Round [954] log likelihood: -27757.224919
EM: Round [955] log likelihood: -27757.224620
EM: Round [956] log likelihood: -27757.224324
EM: Round [957] log likelihood: -27757.224029
EM: Round [958] log likelihood: -27757.223736
EM: Round [959] log likelihood: -27757.223445
EM: Round [960] log likelihood: -27757.223156
EM: Round [961] log likelihood: -27757.222868
EM: Round [962] log likelihood: -27757.222582
EM: Round [963] log likelihood: -27757.222298
EM: Round [964] log likelihood: -27757.222015
EM: Round [965] log likelihood: -27757.221735
EM: Round [966] log likelihood: -27757.221456
EM: Round [967] log likelihood: -27757.221178
EM: Round [968] log likelihood: -27757.220903
EM: Round [969] log likelihood: -27757.220629
EM: Round [970] log likelihood: -27757.220356
EM: Round [971] log likelihood: -27757.220086
EM: Round [972] log likelihood: -27757.219817
EM: Round [973] log likelihood: -27757.219549
EM: Round [974] log likelihood: -27757.219284
EM: Round [975] log likelihood: -27757.219020
EM: Round [976] log likelihood: -27757.218757
EM: Round [977] log likelihood: -27757.218496
EM: Round [978] log likelihood: -27757.218237
EM: Round [979] log likelihood: -27757.217979
EM: Round [980] log likelihood: -27757.217723
EM: Round [981] log likelihood: -27757.217468
EM: Round [982] log likelihood: -27757.217215
EM: Round [983] log likelihood: -27757.216963
EM: Round [984] log likelihood: -27757.216713
EM: Round [985] log likelihood: -27757.216465
EM: Round [986] log likelihood: -27757.216218
EM: Round [987] log likelihood: -27757.215972
EM: Round [988] log likelihood: -27757.215728
EM: Round [989] log likelihood: -27757.215485
EM: Round [990] log likelihood: -27757.215244
EM: Round [991] log likelihood: -27757.215005
EM: Round [992] log likelihood: -27757.214766
EM: Round [993] log likelihood: -27757.214530
EM: Round [994] log likelihood: -27757.214294
EM: Round [995] log likelihood: -27757.214061
EM: Round [996] log likelihood: -27757.213828
EM: Round [997] log likelihood: -27757.213597
EM: Round [998] log likelihood: -27757.213367
EM: Round [999] log likelihood: -27757.213139
EM: Round [1000] log likelihood: -27757.212912
EM: Round [1001] log likelihood: -27757.212687
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir
-done, see /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -24629.476793
EM: Round [1] log likelihood: -24531.877036
EM: Round [2] log likelihood: -24530.785641
EM: Round [3] log likelihood: -24530.780129
EM: Round [4] log likelihood: -24530.780106
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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 209192447
Execution Time = 4.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/fi_workdir/microH.dat
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.tExeCh6s5b/fi_workdir/microH.dat /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/microH.dat /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.tExeCh6s5b --json_outfile /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.tExeCh6s5b --json_outfile /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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 [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory