Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/df494e0b97d2a0899527f8115611f8/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/df494e0b97d2a0899527f8115611f8/tih_rna_sample_00628_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/09bf8da0866a4eaee13bc0b43da8e7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/09bf8da0866a4eaee13bc0b43da8e7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/6d9308e395b56b89b9272fb8771e9f/tih_rna_sample_00628_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00628_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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 tih_rna_sample_00628_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/cytoBand.txt
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00628_B23MVV7LT4_1.star --out_dir /tmp/nxf.DXIqsdmJjc/fi_workdir --reads "/tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:30:04 ..... started STAR run
Jun 08 10:30:04 ..... loading genome
Jun 08 10:31:48 ... generating Suffix Array index
Jun 08 10:35:40 ... completed Suffix Array index
Jun 08 10:35:40 ..... processing annotations GTF
Jun 08 10:35:41 ..... inserting junctions into the genome indices
Jun 08 10:36:42 ..... started mapping
Jun 08 11:59:56 ..... finished mapping
Jun 08 11:59:58 ..... started sorting BAM
Jun 08 11:59:59 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 89.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00628_B23MVV7LT4_1.star --out_dir /tmp/nxf.DXIqsdmJjc/fi_workdir --reads "/tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
12:00:08 : INFO : Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1480000] -done parsing /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'seq-similar region overlap' => 34,
'per_id < 96' => 3366,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34,
'exons hit < 2' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 16,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 87,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 54,
'small anchor length' => 90,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 472,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 16,
' ** passed ** ' => 15847,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
'excessive soft clipping' => 7902,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 203,
'num genes matched < 2' => 1266,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30
};
-writing fusion junction support info.
Execution Time = 0.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[23000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[25000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[29000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 14959,
'seq similar region alignment' => 19358
};
Execution Time = 1.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7306.158642
EM: Round [1] log likelihood: -7294.734291
EM: Round [2] log likelihood: -7294.200537
EM: Round [3] log likelihood: -7293.842685
EM: Round [4] log likelihood: -7293.562309
EM: Round [5] log likelihood: -7293.328182
EM: Round [6] log likelihood: -7293.125281
EM: Round [7] log likelihood: -7292.945538
EM: Round [8] log likelihood: -7292.784107
EM: Round [9] log likelihood: -7292.637748
EM: Round [10] log likelihood: -7292.504092
EM: Round [11] log likelihood: -7292.381287
EM: Round [12] log likelihood: -7292.267824
EM: Round [13] log likelihood: -7292.162444
EM: Round [14] log likelihood: -7292.064077
EM: Round [15] log likelihood: -7291.971814
EM: Round [16] log likelihood: -7291.884877
EM: Round [17] log likelihood: -7291.802604
EM: Round [18] log likelihood: -7291.724427
EM: Round [19] log likelihood: -7291.649866
EM: Round [20] log likelihood: -7291.578508
EM: Round [21] log likelihood: -7291.510007
EM: Round [22] log likelihood: -7291.444064
EM: Round [23] log likelihood: -7291.380428
EM: Round [24] log likelihood: -7291.318885
EM: Round [25] log likelihood: -7291.259249
EM: Round [26] log likelihood: -7291.201366
EM: Round [27] log likelihood: -7291.145099
EM: Round [28] log likelihood: -7291.090332
EM: Round [29] log likelihood: -7291.036964
EM: Round [30] log likelihood: -7290.984908
EM: Round [31] log likelihood: -7290.934085
EM: Round [32] log likelihood: -7290.884429
EM: Round [33] log likelihood: -7290.835878
EM: Round [34] log likelihood: -7290.788378
EM: Round [35] log likelihood: -7290.741881
EM: Round [36] log likelihood: -7290.696343
EM: Round [37] log likelihood: -7290.651724
EM: Round [38] log likelihood: -7290.607986
EM: Round [39] log likelihood: -7290.565096
EM: Round [40] log likelihood: -7290.523024
EM: Round [41] log likelihood: -7290.481739
EM: Round [42] log likelihood: -7290.441214
EM: Round [43] log likelihood: -7290.401425
EM: Round [44] log likelihood: -7290.362347
EM: Round [45] log likelihood: -7290.323958
EM: Round [46] log likelihood: -7290.286236
EM: Round [47] log likelihood: -7290.249162
EM: Round [48] log likelihood: -7290.212716
EM: Round [49] log likelihood: -7290.176880
EM: Round [50] log likelihood: -7290.141637
EM: Round [51] log likelihood: -7290.106970
EM: Round [52] log likelihood: -7290.072864
EM: Round [53] log likelihood: -7290.039303
EM: Round [54] log likelihood: -7290.006273
EM: Round [55] log likelihood: -7289.973760
EM: Round [56] log likelihood: -7289.941750
EM: Round [57] log likelihood: -7289.910232
EM: Round [58] log likelihood: -7289.879192
EM: Round [59] log likelihood: -7289.848619
EM: Round [60] log likelihood: -7289.818502
EM: Round [61] log likelihood: -7289.788829
EM: Round [62] log likelihood: -7289.759590
EM: Round [63] log likelihood: -7289.730775
EM: Round [64] log likelihood: -7289.702374
EM: Round [65] log likelihood: -7289.674378
EM: Round [66] log likelihood: -7289.646777
EM: Round [67] log likelihood: -7289.619563
EM: Round [68] log likelihood: -7289.592727
EM: Round [69] log likelihood: -7289.566260
EM: Round [70] log likelihood: -7289.540156
EM: Round [71] log likelihood: -7289.514405
EM: Round [72] log likelihood: -7289.489001
EM: Round [73] log likelihood: -7289.463937
EM: Round [74] log likelihood: -7289.439205
EM: Round [75] log likelihood: -7289.414798
EM: Round [76] log likelihood: -7289.390710
EM: Round [77] log likelihood: -7289.366935
EM: Round [78] log likelihood: -7289.343466
EM: Round [79] log likelihood: -7289.320298
EM: Round [80] log likelihood: -7289.297424
EM: Round [81] log likelihood: -7289.274838
EM: Round [82] log likelihood: -7289.252536
EM: Round [83] log likelihood: -7289.230512
EM: Round [84] log likelihood: -7289.208760
EM: Round [85] log likelihood: -7289.187276
EM: Round [86] log likelihood: -7289.166054
EM: Round [87] log likelihood: -7289.145090
EM: Round [88] log likelihood: -7289.124379
EM: Round [89] log likelihood: -7289.103917
EM: Round [90] log likelihood: -7289.083699
EM: Round [91] log likelihood: -7289.063721
EM: Round [92] log likelihood: -7289.043978
EM: Round [93] log likelihood: -7289.024467
EM: Round [94] log likelihood: -7289.005183
EM: Round [95] log likelihood: -7288.986123
EM: Round [96] log likelihood: -7288.967283
EM: Round [97] log likelihood: -7288.948659
EM: Round [98] log likelihood: -7288.930247
EM: Round [99] log likelihood: -7288.912044
EM: Round [100] log likelihood: -7288.894046
EM: Round [101] log likelihood: -7288.876251
EM: Round [102] log likelihood: -7288.858654
EM: Round [103] log likelihood: -7288.841253
EM: Round [104] log likelihood: -7288.824045
EM: Round [105] log likelihood: -7288.807026
EM: Round [106] log likelihood: -7288.790193
EM: Round [107] log likelihood: -7288.773544
EM: Round [108] log likelihood: -7288.757076
EM: Round [109] log likelihood: -7288.740785
EM: Round [110] log likelihood: -7288.724669
EM: Round [111] log likelihood: -7288.708726
EM: Round [112] log likelihood: -7288.692952
EM: Round [113] log likelihood: -7288.677346
EM: Round [114] log likelihood: -7288.661905
EM: Round [115] log likelihood: -7288.646625
EM: Round [116] log likelihood: -7288.631506
EM: Round [117] log likelihood: -7288.616544
EM: Round [118] log likelihood: -7288.601737
EM: Round [119] log likelihood: -7288.587083
EM: Round [120] log likelihood: -7288.572580
EM: Round [121] log likelihood: -7288.558226
EM: Round [122] log likelihood: -7288.544018
EM: Round [123] log likelihood: -7288.529954
EM: Round [124] log likelihood: -7288.516033
EM: Round [125] log likelihood: -7288.502252
EM: Round [126] log likelihood: -7288.488609
EM: Round [127] log likelihood: -7288.475103
EM: Round [128] log likelihood: -7288.461731
EM: Round [129] log likelihood: -7288.448492
EM: Round [130] log likelihood: -7288.435384
EM: Round [131] log likelihood: -7288.422405
EM: Round [132] log likelihood: -7288.409553
EM: Round [133] log likelihood: -7288.396827
EM: Round [134] log likelihood: -7288.384225
EM: Round [135] log likelihood: -7288.371746
EM: Round [136] log likelihood: -7288.359387
EM: Round [137] log likelihood: -7288.347147
EM: Round [138] log likelihood: -7288.335024
EM: Round [139] log likelihood: -7288.323018
EM: Round [140] log likelihood: -7288.311126
EM: Round [141] log likelihood: -7288.299347
EM: Round [142] log likelihood: -7288.287680
EM: Round [143] log likelihood: -7288.276123
EM: Round [144] log likelihood: -7288.264675
EM: Round [145] log likelihood: -7288.253334
EM: Round [146] log likelihood: -7288.242099
EM: Round [147] log likelihood: -7288.230968
EM: Round [148] log likelihood: -7288.219941
EM: Round [149] log likelihood: -7288.209017
EM: Round [150] log likelihood: -7288.198193
EM: Round [151] log likelihood: -7288.187468
EM: Round [152] log likelihood: -7288.176842
EM: Round [153] log likelihood: -7288.166313
EM: Round [154] log likelihood: -7288.155880
EM: Round [155] log likelihood: -7288.145542
EM: Round [156] log likelihood: -7288.135297
EM: Round [157] log likelihood: -7288.125145
EM: Round [158] log likelihood: -7288.115084
EM: Round [159] log likelihood: -7288.105114
EM: Round [160] log likelihood: -7288.095233
EM: Round [161] log likelihood: -7288.085440
EM: Round [162] log likelihood: -7288.075734
EM: Round [163] log likelihood: -7288.066115
EM: Round [164] log likelihood: -7288.056580
EM: Round [165] log likelihood: -7288.047130
EM: Round [166] log likelihood: -7288.037763
EM: Round [167] log likelihood: -7288.028478
EM: Round [168] log likelihood: -7288.019274
EM: Round [169] log likelihood: -7288.010150
EM: Round [170] log likelihood: -7288.001106
EM: Round [171] log likelihood: -7287.992141
EM: Round [172] log likelihood: -7287.983253
EM: Round [173] log likelihood: -7287.974442
EM: Round [174] log likelihood: -7287.965706
EM: Round [175] log likelihood: -7287.957046
EM: Round [176] log likelihood: -7287.948460
EM: Round [177] log likelihood: -7287.939947
EM: Round [178] log likelihood: -7287.931507
EM: Round [179] log likelihood: -7287.923138
EM: Round [180] log likelihood: -7287.914840
EM: Round [181] log likelihood: -7287.906613
EM: Round [182] log likelihood: -7287.898455
EM: Round [183] log likelihood: -7287.890365
EM: Round [184] log likelihood: -7287.882344
EM: Round [185] log likelihood: -7287.874389
EM: Round [186] log likelihood: -7287.866501
EM: Round [187] log likelihood: -7287.858679
EM: Round [188] log likelihood: -7287.850922
EM: Round [189] log likelihood: -7287.843229
EM: Round [190] log likelihood: -7287.835600
EM: Round [191] log likelihood: -7287.828033
EM: Round [192] log likelihood: -7287.820529
EM: Round [193] log likelihood: -7287.813087
EM: Round [194] log likelihood: -7287.805705
EM: Round [195] log likelihood: -7287.798384
EM: Round [196] log likelihood: -7287.791122
EM: Round [197] log likelihood: -7287.783920
EM: Round [198] log likelihood: -7287.776776
EM: Round [199] log likelihood: -7287.769690
EM: Round [200] log likelihood: -7287.762661
EM: Round [201] log likelihood: -7287.755689
EM: Round [202] log likelihood: -7287.748773
EM: Round [203] log likelihood: -7287.741912
EM: Round [204] log likelihood: -7287.735107
EM: Round [205] log likelihood: -7287.728355
EM: Round [206] log likelihood: -7287.721658
EM: Round [207] log likelihood: -7287.715014
EM: Round [208] log likelihood: -7287.708422
EM: Round [209] log likelihood: -7287.701883
EM: Round [210] log likelihood: -7287.695395
EM: Round [211] log likelihood: -7287.688959
EM: Round [212] log likelihood: -7287.682573
EM: Round [213] log likelihood: -7287.676238
EM: Round [214] log likelihood: -7287.669952
EM: Round [215] log likelihood: -7287.663715
EM: Round [216] log likelihood: -7287.657527
EM: Round [217] log likelihood: -7287.651387
EM: Round [218] log likelihood: -7287.645295
EM: Round [219] log likelihood: -7287.639250
EM: Round [220] log likelihood: -7287.633252
EM: Round [221] log likelihood: -7287.627300
EM: Round [222] log likelihood: -7287.621394
EM: Round [223] log likelihood: -7287.615534
EM: Round [224] log likelihood: -7287.609718
EM: Round [225] log likelihood: -7287.603947
EM: Round [226] log likelihood: -7287.598220
EM: Round [227] log likelihood: -7287.592537
EM: Round [228] log likelihood: -7287.586898
EM: Round [229] log likelihood: -7287.581301
EM: Round [230] log likelihood: -7287.575746
EM: Round [231] log likelihood: -7287.570234
EM: Round [232] log likelihood: -7287.564763
EM: Round [233] log likelihood: -7287.559333
EM: Round [234] log likelihood: -7287.553945
EM: Round [235] log likelihood: -7287.548596
EM: Round [236] log likelihood: -7287.543288
EM: Round [237] log likelihood: -7287.538020
EM: Round [238] log likelihood: -7287.532791
EM: Round [239] log likelihood: -7287.527601
EM: Round [240] log likelihood: -7287.522449
EM: Round [241] log likelihood: -7287.517336
EM: Round [242] log likelihood: -7287.512261
EM: Round [243] log likelihood: -7287.507223
EM: Round [244] log likelihood: -7287.502223
EM: Round [245] log likelihood: -7287.497259
EM: Round [246] log likelihood: -7287.492332
EM: Round [247] log likelihood: -7287.487441
EM: Round [248] log likelihood: -7287.482586
EM: Round [249] log likelihood: -7287.477767
EM: Round [250] log likelihood: -7287.472982
EM: Round [251] log likelihood: -7287.468233
EM: Round [252] log likelihood: -7287.463518
EM: Round [253] log likelihood: -7287.458837
EM: Round [254] log likelihood: -7287.454191
EM: Round [255] log likelihood: -7287.449578
EM: Round [256] log likelihood: -7287.444998
EM: Round [257] log likelihood: -7287.440451
EM: Round [258] log likelihood: -7287.435937
EM: Round [259] log likelihood: -7287.431456
EM: Round [260] log likelihood: -7287.427006
EM: Round [261] log likelihood: -7287.422589
EM: Round [262] log likelihood: -7287.418203
EM: Round [263] log likelihood: -7287.413848
EM: Round [264] log likelihood: -7287.409525
EM: Round [265] log likelihood: -7287.405232
EM: Round [266] log likelihood: -7287.400970
EM: Round [267] log likelihood: -7287.396737
EM: Round [268] log likelihood: -7287.392535
EM: Round [269] log likelihood: -7287.388363
EM: Round [270] log likelihood: -7287.384219
EM: Round [271] log likelihood: -7287.380105
EM: Round [272] log likelihood: -7287.376020
EM: Round [273] log likelihood: -7287.371964
EM: Round [274] log likelihood: -7287.367936
EM: Round [275] log likelihood: -7287.363936
EM: Round [276] log likelihood: -7287.359964
EM: Round [277] log likelihood: -7287.356020
EM: Round [278] log likelihood: -7287.352103
EM: Round [279] log likelihood: -7287.348213
EM: Round [280] log likelihood: -7287.344351
EM: Round [281] log likelihood: -7287.340515
EM: Round [282] log likelihood: -7287.336705
EM: Round [283] log likelihood: -7287.332922
EM: Round [284] log likelihood: -7287.329165
EM: Round [285] log likelihood: -7287.325434
EM: Round [286] log likelihood: -7287.321728
EM: Round [287] log likelihood: -7287.318048
EM: Round [288] log likelihood: -7287.314392
EM: Round [289] log likelihood: -7287.310762
EM: Round [290] log likelihood: -7287.307157
EM: Round [291] log likelihood: -7287.303576
EM: Round [292] log likelihood: -7287.300019
EM: Round [293] log likelihood: -7287.296487
EM: Round [294] log likelihood: -7287.292978
EM: Round [295] log likelihood: -7287.289493
EM: Round [296] log likelihood: -7287.286032
EM: Round [297] log likelihood: -7287.282594
EM: Round [298] log likelihood: -7287.279179
EM: Round [299] log likelihood: -7287.275787
EM: Round [300] log likelihood: -7287.272418
EM: Round [301] log likelihood: -7287.269072
EM: Round [302] log likelihood: -7287.265747
EM: Round [303] log likelihood: -7287.262445
EM: Round [304] log likelihood: -7287.259165
EM: Round [305] log likelihood: -7287.255907
EM: Round [306] log likelihood: -7287.252671
EM: Round [307] log likelihood: -7287.249456
EM: Round [308] log likelihood: -7287.246262
EM: Round [309] log likelihood: -7287.243089
EM: Round [310] log likelihood: -7287.239937
EM: Round [311] log likelihood: -7287.236806
EM: Round [312] log likelihood: -7287.233696
EM: Round [313] log likelihood: -7287.230606
EM: Round [314] log likelihood: -7287.227536
EM: Round [315] log likelihood: -7287.224487
EM: Round [316] log likelihood: -7287.221457
EM: Round [317] log likelihood: -7287.218447
EM: Round [318] log likelihood: -7287.215457
EM: Round [319] log likelihood: -7287.212486
EM: Round [320] log likelihood: -7287.209535
EM: Round [321] log likelihood: -7287.206602
EM: Round [322] log likelihood: -7287.203689
EM: Round [323] log likelihood: -7287.200795
EM: Round [324] log likelihood: -7287.197919
EM: Round [325] log likelihood: -7287.195061
EM: Round [326] log likelihood: -7287.192223
EM: Round [327] log likelihood: -7287.189402
EM: Round [328] log likelihood: -7287.186599
EM: Round [329] log likelihood: -7287.183815
EM: Round [330] log likelihood: -7287.181048
EM: Round [331] log likelihood: -7287.178299
EM: Round [332] log likelihood: -7287.175567
EM: Round [333] log likelihood: -7287.172853
EM: Round [334] log likelihood: -7287.170156
EM: Round [335] log likelihood: -7287.167476
EM: Round [336] log likelihood: -7287.164813
EM: Round [337] log likelihood: -7287.162167
EM: Round [338] log likelihood: -7287.159538
EM: Round [339] log likelihood: -7287.156926
EM: Round [340] log likelihood: -7287.154329
EM: Round [341] log likelihood: -7287.151749
EM: Round [342] log likelihood: -7287.149186
EM: Round [343] log likelihood: -7287.146638
EM: Round [344] log likelihood: -7287.144106
EM: Round [345] log likelihood: -7287.141591
EM: Round [346] log likelihood: -7287.139090
EM: Round [347] log likelihood: -7287.136606
EM: Round [348] log likelihood: -7287.134137
EM: Round [349] log likelihood: -7287.131683
EM: Round [350] log likelihood: -7287.129245
EM: Round [351] log likelihood: -7287.126821
EM: Round [352] log likelihood: -7287.124413
EM: Round [353] log likelihood: -7287.122019
EM: Round [354] log likelihood: -7287.119640
EM: Round [355] log likelihood: -7287.117276
EM: Round [356] log likelihood: -7287.114926
EM: Round [357] log likelihood: -7287.112591
EM: Round [358] log likelihood: -7287.110270
EM: Round [359] log likelihood: -7287.107964
EM: Round [360] log likelihood: -7287.105671
EM: Round [361] log likelihood: -7287.103392
EM: Round [362] log likelihood: -7287.101128
EM: Round [363] log likelihood: -7287.098877
EM: Round [364] log likelihood: -7287.096639
EM: Round [365] log likelihood: -7287.094416
EM: Round [366] log likelihood: -7287.092205
EM: Round [367] log likelihood: -7287.090008
EM: Round [368] log likelihood: -7287.087825
EM: Round [369] log likelihood: -7287.085654
EM: Round [370] log likelihood: -7287.083497
EM: Round [371] log likelihood: -7287.081352
EM: Round [372] log likelihood: -7287.079221
EM: Round [373] log likelihood: -7287.077102
EM: Round [374] log likelihood: -7287.074996
EM: Round [375] log likelihood: -7287.072902
EM: Round [376] log likelihood: -7287.070821
EM: Round [377] log likelihood: -7287.068753
EM: Round [378] log likelihood: -7287.066696
EM: Round [379] log likelihood: -7287.064652
EM: Round [380] log likelihood: -7287.062620
EM: Round [381] log likelihood: -7287.060600
EM: Round [382] log likelihood: -7287.058592
EM: Round [383] log likelihood: -7287.056596
EM: Round [384] log likelihood: -7287.054611
EM: Round [385] log likelihood: -7287.052638
EM: Round [386] log likelihood: -7287.050677
EM: Round [387] log likelihood: -7287.048728
EM: Round [388] log likelihood: -7287.046789
EM: Round [389] log likelihood: -7287.044862
EM: Round [390] log likelihood: -7287.042947
EM: Round [391] log likelihood: -7287.041042
EM: Round [392] log likelihood: -7287.039149
EM: Round [393] log likelihood: -7287.037266
EM: Round [394] log likelihood: -7287.035395
EM: Round [395] log likelihood: -7287.033534
EM: Round [396] log likelihood: -7287.031684
EM: Round [397] log likelihood: -7287.029845
EM: Round [398] log likelihood: -7287.028017
EM: Round [399] log likelihood: -7287.026199
EM: Round [400] log likelihood: -7287.024391
EM: Round [401] log likelihood: -7287.022594
EM: Round [402] log likelihood: -7287.020807
EM: Round [403] log likelihood: -7287.019030
EM: Round [404] log likelihood: -7287.017264
EM: Round [405] log likelihood: -7287.015508
EM: Round [406] log likelihood: -7287.013761
EM: Round [407] log likelihood: -7287.012025
EM: Round [408] log likelihood: -7287.010298
EM: Round [409] log likelihood: -7287.008581
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EM: Round [866] log likelihood: -7286.688661
EM: Round [867] log likelihood: -7286.688393
EM: Round [868] log likelihood: -7286.688125
EM: Round [869] log likelihood: -7286.687857
EM: Round [870] log likelihood: -7286.687591
EM: Round [871] log likelihood: -7286.687325
EM: Round [872] log likelihood: -7286.687060
EM: Round [873] log likelihood: -7286.686796
EM: Round [874] log likelihood: -7286.686532
EM: Round [875] log likelihood: -7286.686269
EM: Round [876] log likelihood: -7286.686007
EM: Round [877] log likelihood: -7286.685745
EM: Round [878] log likelihood: -7286.685484
EM: Round [879] log likelihood: -7286.685224
EM: Round [880] log likelihood: -7286.684965
EM: Round [881] log likelihood: -7286.684706
EM: Round [882] log likelihood: -7286.684448
EM: Round [883] log likelihood: -7286.684190
EM: Round [884] log likelihood: -7286.683934
EM: Round [885] log likelihood: -7286.683677
EM: Round [886] log likelihood: -7286.683422
EM: Round [887] log likelihood: -7286.683167
EM: Round [888] log likelihood: -7286.682913
EM: Round [889] log likelihood: -7286.682660
EM: Round [890] log likelihood: -7286.682407
EM: Round [891] log likelihood: -7286.682155
EM: Round [892] log likelihood: -7286.681904
EM: Round [893] log likelihood: -7286.681653
EM: Round [894] log likelihood: -7286.681403
EM: Round [895] log likelihood: -7286.681154
EM: Round [896] log likelihood: -7286.680905
EM: Round [897] log likelihood: -7286.680657
EM: Round [898] log likelihood: -7286.680409
EM: Round [899] log likelihood: -7286.680162
EM: Round [900] log likelihood: -7286.679916
EM: Round [901] log likelihood: -7286.679670
EM: Round [902] log likelihood: -7286.679425
EM: Round [903] log likelihood: -7286.679181
EM: Round [904] log likelihood: -7286.678937
EM: Round [905] log likelihood: -7286.678694
EM: Round [906] log likelihood: -7286.678452
EM: Round [907] log likelihood: -7286.678210
EM: Round [908] log likelihood: -7286.677969
EM: Round [909] log likelihood: -7286.677728
EM: Round [910] log likelihood: -7286.677488
EM: Round [911] log likelihood: -7286.677249
EM: Round [912] log likelihood: -7286.677010
EM: Round [913] log likelihood: -7286.676771
EM: Round [914] log likelihood: -7286.676534
EM: Round [915] log likelihood: -7286.676297
EM: Round [916] log likelihood: -7286.676060
EM: Round [917] log likelihood: -7286.675825
EM: Round [918] log likelihood: -7286.675589
EM: Round [919] log likelihood: -7286.675355
EM: Round [920] log likelihood: -7286.675121
EM: Round [921] log likelihood: -7286.674887
EM: Round [922] log likelihood: -7286.674654
EM: Round [923] log likelihood: -7286.674422
EM: Round [924] log likelihood: -7286.674190
EM: Round [925] log likelihood: -7286.673959
EM: Round [926] log likelihood: -7286.673728
EM: Round [927] log likelihood: -7286.673498
EM: Round [928] log likelihood: -7286.673269
EM: Round [929] log likelihood: -7286.673040
EM: Round [930] log likelihood: -7286.672812
EM: Round [931] log likelihood: -7286.672584
EM: Round [932] log likelihood: -7286.672357
EM: Round [933] log likelihood: -7286.672130
EM: Round [934] log likelihood: -7286.671904
EM: Round [935] log likelihood: -7286.671678
EM: Round [936] log likelihood: -7286.671453
EM: Round [937] log likelihood: -7286.671229
EM: Round [938] log likelihood: -7286.671005
EM: Round [939] log likelihood: -7286.670781
EM: Round [940] log likelihood: -7286.670559
EM: Round [941] log likelihood: -7286.670336
EM: Round [942] log likelihood: -7286.670115
EM: Round [943] log likelihood: -7286.669893
EM: Round [944] log likelihood: -7286.669673
EM: Round [945] log likelihood: -7286.669452
EM: Round [946] log likelihood: -7286.669233
EM: Round [947] log likelihood: -7286.669014
EM: Round [948] log likelihood: -7286.668795
EM: Round [949] log likelihood: -7286.668577
EM: Round [950] log likelihood: -7286.668359
EM: Round [951] log likelihood: -7286.668142
EM: Round [952] log likelihood: -7286.667926
EM: Round [953] log likelihood: -7286.667710
EM: Round [954] log likelihood: -7286.667494
EM: Round [955] log likelihood: -7286.667279
EM: Round [956] log likelihood: -7286.667065
EM: Round [957] log likelihood: -7286.666851
EM: Round [958] log likelihood: -7286.666637
EM: Round [959] log likelihood: -7286.666424
EM: Round [960] log likelihood: -7286.666212
EM: Round [961] log likelihood: -7286.666000
EM: Round [962] log likelihood: -7286.665789
EM: Round [963] log likelihood: -7286.665578
EM: Round [964] log likelihood: -7286.665367
EM: Round [965] log likelihood: -7286.665157
EM: Round [966] log likelihood: -7286.664947
EM: Round [967] log likelihood: -7286.664738
EM: Round [968] log likelihood: -7286.664530
EM: Round [969] log likelihood: -7286.664322
EM: Round [970] log likelihood: -7286.664114
EM: Round [971] log likelihood: -7286.663907
EM: Round [972] log likelihood: -7286.663700
EM: Round [973] log likelihood: -7286.663494
EM: Round [974] log likelihood: -7286.663289
EM: Round [975] log likelihood: -7286.663083
EM: Round [976] log likelihood: -7286.662879
EM: Round [977] log likelihood: -7286.662674
EM: Round [978] log likelihood: -7286.662471
EM: Round [979] log likelihood: -7286.662267
EM: Round [980] log likelihood: -7286.662064
EM: Round [981] log likelihood: -7286.661862
EM: Round [982] log likelihood: -7286.661660
EM: Round [983] log likelihood: -7286.661458
EM: Round [984] log likelihood: -7286.661257
EM: Round [985] log likelihood: -7286.661057
EM: Round [986] log likelihood: -7286.660857
EM: Round [987] log likelihood: -7286.660657
EM: Round [988] log likelihood: -7286.660458
EM: Round [989] log likelihood: -7286.660259
EM: Round [990] log likelihood: -7286.660061
EM: Round [991] log likelihood: -7286.659863
EM: Round [992] log likelihood: -7286.659665
EM: Round [993] log likelihood: -7286.659468
EM: Round [994] log likelihood: -7286.659272
EM: Round [995] log likelihood: -7286.659075
EM: Round [996] log likelihood: -7286.658880
EM: Round [997] log likelihood: -7286.658685
EM: Round [998] log likelihood: -7286.658490
EM: Round [999] log likelihood: -7286.658295
EM: Round [1000] log likelihood: -7286.658101
EM: Round [1001] log likelihood: -7286.657908
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/tih_rna_sample_00628_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa > /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir
-done, see /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4842.850267
EM: Round [1] log likelihood: -4842.413175
EM: Round [2] log likelihood: -4842.410535
EM: Round [3] log likelihood: -4842.409504
EM: Round [4] log likelihood: -4842.408480
EM: Round [5] log likelihood: -4842.407458
EM: Round [6] log likelihood: -4842.406438
EM: Round [7] log likelihood: -4842.405420
EM: Round [8] log likelihood: -4842.404405
EM: Round [9] log likelihood: -4842.403391
EM: Round [10] log likelihood: -4842.402380
EM: Round [11] log likelihood: -4842.401370
EM: Round [12] log likelihood: -4842.400363
EM: Round [13] log likelihood: -4842.399357
EM: Round [14] log likelihood: -4842.398354
EM: Round [15] log likelihood: -4842.397353
EM: Round [16] log likelihood: -4842.396354
EM: Round [17] log likelihood: -4842.395356
EM: Round [18] log likelihood: -4842.394361
EM: Round [19] log likelihood: -4842.393368
EM: Round [20] log likelihood: -4842.392377
EM: Round [21] log likelihood: -4842.391388
EM: Round [22] log likelihood: -4842.390401
EM: Round [23] log likelihood: -4842.389416
EM: Round [24] log likelihood: -4842.388432
EM: Round [25] log likelihood: -4842.387451
EM: Round [26] log likelihood: -4842.386472
EM: Round [27] log likelihood: -4842.385495
EM: Round [28] log likelihood: -4842.384519
EM: Round [29] log likelihood: -4842.383546
EM: Round [30] log likelihood: -4842.382575
EM: Round [31] log likelihood: -4842.381605
EM: Round [32] log likelihood: -4842.380638
EM: Round [33] log likelihood: -4842.379672
EM: Round [34] log likelihood: -4842.378709
EM: Round [35] log likelihood: -4842.377747
EM: Round [36] log likelihood: -4842.376787
EM: Round [37] log likelihood: -4842.375829
EM: Round [38] log likelihood: -4842.374873
EM: Round [39] log likelihood: -4842.373919
EM: Round [40] log likelihood: -4842.372967
EM: Round [41] log likelihood: -4842.372017
EM: Round [42] log likelihood: -4842.371068
EM: Round [43] log likelihood: -4842.370122
EM: Round [44] log likelihood: -4842.369177
EM: Round [45] log likelihood: -4842.368234
EM: Round [46] log likelihood: -4842.367293
EM: Round [47] log likelihood: -4842.366354
EM: Round [48] log likelihood: -4842.365417
EM: Round [49] log likelihood: -4842.364482
EM: Round [50] log likelihood: -4842.363548
EM: Round [51] log likelihood: -4842.362616
EM: Round [52] log likelihood: -4842.361687
EM: Round [53] log likelihood: -4842.360758
EM: Round [54] log likelihood: -4842.359832
EM: Round [55] log likelihood: -4842.358908
EM: Round [56] log likelihood: -4842.357985
EM: Round [57] log likelihood: -4842.357064
EM: Round [58] log likelihood: -4842.356145
EM: Round [59] log likelihood: -4842.355228
EM: Round [60] log likelihood: -4842.354313
EM: Round [61] log likelihood: -4842.353399
EM: Round [62] log likelihood: -4842.352487
EM: Round [63] log likelihood: -4842.351577
EM: Round [64] log likelihood: -4842.350669
EM: Round [65] log likelihood: -4842.349762
EM: Round [66] log likelihood: -4842.348857
EM: Round [67] log likelihood: -4842.347954
EM: Round [68] log likelihood: -4842.347053
EM: Round [69] log likelihood: -4842.346153
EM: Round [70] log likelihood: -4842.345255
EM: Round [71] log likelihood: -4842.344359
EM: Round [72] log likelihood: -4842.343465
EM: Round [73] log likelihood: -4842.342572
EM: Round [74] log likelihood: -4842.341681
EM: Round [75] log likelihood: -4842.340792
EM: Round [76] log likelihood: -4842.339904
EM: Round [77] log likelihood: -4842.339019
EM: Round [78] log likelihood: -4842.338134
EM: Round [79] log likelihood: -4842.337252
EM: Round [80] log likelihood: -4842.336371
EM: Round [81] log likelihood: -4842.335492
EM: Round [82] log likelihood: -4842.334615
EM: Round [83] log likelihood: -4842.333739
EM: Round [84] log likelihood: -4842.332865
EM: Round [85] log likelihood: -4842.331993
EM: Round [86] log likelihood: -4842.331122
EM: Round [87] log likelihood: -4842.330253
EM: Round [88] log likelihood: -4842.329385
EM: Round [89] log likelihood: -4842.328520
EM: Round [90] log likelihood: -4842.327655
EM: Round [91] log likelihood: -4842.326793
EM: Round [92] log likelihood: -4842.325932
EM: Round [93] log likelihood: -4842.325073
EM: Round [94] log likelihood: -4842.324215
EM: Round [95] log likelihood: -4842.323359
EM: Round [96] log likelihood: -4842.322505
EM: Round [97] log likelihood: -4842.321652
EM: Round [98] log likelihood: -4842.320801
EM: Round [99] log likelihood: -4842.319951
EM: Round [100] log likelihood: -4842.319104
EM: Round [101] log likelihood: -4842.318257
EM: Round [102] log likelihood: -4842.317412
EM: Round [103] log likelihood: -4842.316569
EM: Round [104] log likelihood: -4842.315728
EM: Round [105] log likelihood: -4842.314888
EM: Round [106] log likelihood: -4842.314049
EM: Round [107] log likelihood: -4842.313212
EM: Round [108] log likelihood: -4842.312377
EM: Round [109] log likelihood: -4842.311543
EM: Round [110] log likelihood: -4842.310711
EM: Round [111] log likelihood: -4842.309880
EM: Round [112] log likelihood: -4842.309051
EM: Round [113] log likelihood: -4842.308224
EM: Round [114] log likelihood: -4842.307398
EM: Round [115] log likelihood: -4842.306573
EM: Round [116] log likelihood: -4842.305750
EM: Round [117] log likelihood: -4842.304929
EM: Round [118] log likelihood: -4842.304109
EM: Round [119] log likelihood: -4842.303290
EM: Round [120] log likelihood: -4842.302473
EM: Round [121] log likelihood: -4842.301658
EM: Round [122] log likelihood: -4842.300844
EM: Round [123] log likelihood: -4842.300032
EM: Round [124] log likelihood: -4842.299221
EM: Round [125] log likelihood: -4842.298411
EM: Round [126] log likelihood: -4842.297604
EM: Round [127] log likelihood: -4842.296797
EM: Round [128] log likelihood: -4842.295992
EM: Round [129] log likelihood: -4842.295189
EM: Round [130] log likelihood: -4842.294387
EM: Round [131] log likelihood: -4842.293586
EM: Round [132] log likelihood: -4842.292787
EM: Round [133] log likelihood: -4842.291990
EM: Round [134] log likelihood: -4842.291194
EM: Round [135] log likelihood: -4842.290399
EM: Round [136] log likelihood: -4842.289606
EM: Round [137] log likelihood: -4842.288814
EM: Round [138] log likelihood: -4842.288024
EM: Round [139] log likelihood: -4842.287235
EM: Round [140] log likelihood: -4842.286447
EM: Round [141] log likelihood: -4842.285661
EM: Round [142] log likelihood: -4842.284877
EM: Round [143] log likelihood: -4842.284094
EM: Round [144] log likelihood: -4842.283312
EM: Round [145] log likelihood: -4842.282531
EM: Round [146] log likelihood: -4842.281753
EM: Round [147] log likelihood: -4842.280975
EM: Round [148] log likelihood: -4842.280199
EM: Round [149] log likelihood: -4842.279424
EM: Round [150] log likelihood: -4842.278651
EM: Round [151] log likelihood: -4842.277879
EM: Round [152] log likelihood: -4842.277109
EM: Round [153] log likelihood: -4842.276339
EM: Round [154] log likelihood: -4842.275572
EM: Round [155] log likelihood: -4842.274805
EM: Round [156] log likelihood: -4842.274040
EM: Round [157] log likelihood: -4842.273277
EM: Round [158] log likelihood: -4842.272515
EM: Round [159] log likelihood: -4842.271754
EM: Round [160] log likelihood: -4842.270994
EM: Round [161] log likelihood: -4842.270236
EM: Round [162] log likelihood: -4842.269479
EM: Round [163] log likelihood: -4842.268724
EM: Round [164] log likelihood: -4842.267970
EM: Round [165] log likelihood: -4842.267217
EM: Round [166] log likelihood: -4842.266466
EM: Round [167] log likelihood: -4842.265716
EM: Round [168] log likelihood: -4842.264967
EM: Round [169] log likelihood: -4842.264220
EM: Round [170] log likelihood: -4842.263474
EM: Round [171] log likelihood: -4842.262729
EM: Round [172] log likelihood: -4842.261985
EM: Round [173] log likelihood: -4842.261243
EM: Round [174] log likelihood: -4842.260503
EM: Round [175] log likelihood: -4842.259763
EM: Round [176] log likelihood: -4842.259025
EM: Round [177] log likelihood: -4842.258288
EM: Round [178] log likelihood: -4842.257553
EM: Round [179] log likelihood: -4842.256818
EM: Round [180] log likelihood: -4842.256085
EM: Round [181] log likelihood: -4842.255354
EM: Round [182] log likelihood: -4842.254623
EM: Round [183] log likelihood: -4842.253894
EM: Round [184] log likelihood: -4842.253167
EM: Round [185] log likelihood: -4842.252440
EM: Round [186] log likelihood: -4842.251715
EM: Round [187] log likelihood: -4842.250991
EM: Round [188] log likelihood: -4842.250268
EM: Round [189] log likelihood: -4842.249547
EM: Round [190] log likelihood: -4842.248827
EM: Round [191] log likelihood: -4842.248108
EM: Round [192] log likelihood: -4842.247390
EM: Round [193] log likelihood: -4842.246674
EM: Round [194] log likelihood: -4842.245959
EM: Round [195] log likelihood: -4842.245245
EM: Round [196] log likelihood: -4842.244532
EM: Round [197] log likelihood: -4842.243821
EM: Round [198] log likelihood: -4842.243111
EM: Round [199] log likelihood: -4842.242402
EM: Round [200] log likelihood: -4842.241694
EM: Round [201] log likelihood: -4842.240988
EM: Round [202] log likelihood: -4842.240282
EM: Round [203] log likelihood: -4842.239578
EM: Round [204] log likelihood: -4842.238876
EM: Round [205] log likelihood: -4842.238174
EM: Round [206] log likelihood: -4842.237474
EM: Round [207] log likelihood: -4842.236775
EM: Round [208] log likelihood: -4842.236077
EM: Round [209] log likelihood: -4842.235380
EM: Round [210] log likelihood: -4842.234684
EM: Round [211] log likelihood: -4842.233990
EM: Round [212] log likelihood: -4842.233297
EM: Round [213] log likelihood: -4842.232605
EM: Round [214] log likelihood: -4842.231914
EM: Round [215] log likelihood: -4842.231225
EM: Round [216] log likelihood: -4842.230536
EM: Round [217] log likelihood: -4842.229849
EM: Round [218] log likelihood: -4842.229163
EM: Round [219] log likelihood: -4842.228479
EM: Round [220] log likelihood: -4842.227795
EM: Round [221] log likelihood: -4842.227112
EM: Round [222] log likelihood: -4842.226431
EM: Round [223] log likelihood: -4842.225751
EM: Round [224] log likelihood: -4842.225072
EM: Round [225] log likelihood: -4842.224394
EM: Round [226] log likelihood: -4842.223718
EM: Round [227] log likelihood: -4842.223042
EM: Round [228] log likelihood: -4842.222368
EM: Round [229] log likelihood: -4842.221695
EM: Round [230] log likelihood: -4842.221023
EM: Round [231] log likelihood: -4842.220352
EM: Round [232] log likelihood: -4842.219682
EM: Round [233] log likelihood: -4842.219014
EM: Round [234] log likelihood: -4842.218346
EM: Round [235] log likelihood: -4842.217680
EM: Round [236] log likelihood: -4842.217015
EM: Round [237] log likelihood: -4842.216351
EM: Round [238] log likelihood: -4842.215688
EM: Round [239] log likelihood: -4842.215026
EM: Round [240] log likelihood: -4842.214365
EM: Round [241] log likelihood: -4842.213705
EM: Round [242] log likelihood: -4842.213047
EM: Round [243] log likelihood: -4842.212390
EM: Round [244] log likelihood: -4842.211733
EM: Round [245] log likelihood: -4842.211078
EM: Round [246] log likelihood: -4842.210424
EM: Round [247] log likelihood: -4842.209771
EM: Round [248] log likelihood: -4842.209120
EM: Round [249] log likelihood: -4842.208469
EM: Round [250] log likelihood: -4842.207819
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EM: Round [713] log likelihood: -4841.993646
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EM: Round [715] log likelihood: -4841.992998
EM: Round [716] log likelihood: -4841.992674
EM: Round [717] log likelihood: -4841.992351
EM: Round [718] log likelihood: -4841.992028
EM: Round [719] log likelihood: -4841.991706
EM: Round [720] log likelihood: -4841.991384
EM: Round [721] log likelihood: -4841.991063
EM: Round [722] log likelihood: -4841.990742
EM: Round [723] log likelihood: -4841.990421
EM: Round [724] log likelihood: -4841.990101
EM: Round [725] log likelihood: -4841.989782
EM: Round [726] log likelihood: -4841.989462
EM: Round [727] log likelihood: -4841.989144
EM: Round [728] log likelihood: -4841.988825
EM: Round [729] log likelihood: -4841.988507
EM: Round [730] log likelihood: -4841.988190
EM: Round [731] log likelihood: -4841.987873
EM: Round [732] log likelihood: -4841.987556
EM: Round [733] log likelihood: -4841.987240
EM: Round [734] log likelihood: -4841.986924
EM: Round [735] log likelihood: -4841.986609
EM: Round [736] log likelihood: -4841.986294
EM: Round [737] log likelihood: -4841.985979
EM: Round [738] log likelihood: -4841.985665
EM: Round [739] log likelihood: -4841.985351
EM: Round [740] log likelihood: -4841.985038
EM: Round [741] log likelihood: -4841.984725
EM: Round [742] log likelihood: -4841.984413
EM: Round [743] log likelihood: -4841.984101
EM: Round [744] log likelihood: -4841.983789
EM: Round [745] log likelihood: -4841.983478
EM: Round [746] log likelihood: -4841.983168
EM: Round [747] log likelihood: -4841.982857
EM: Round [748] log likelihood: -4841.982547
EM: Round [749] log likelihood: -4841.982238
EM: Round [750] log likelihood: -4841.981929
EM: Round [751] log likelihood: -4841.981620
EM: Round [752] log likelihood: -4841.981312
EM: Round [753] log likelihood: -4841.981004
EM: Round [754] log likelihood: -4841.980697
EM: Round [755] log likelihood: -4841.980390
EM: Round [756] log likelihood: -4841.980083
EM: Round [757] log likelihood: -4841.979777
EM: Round [758] log likelihood: -4841.979471
EM: Round [759] log likelihood: -4841.979166
EM: Round [760] log likelihood: -4841.978861
EM: Round [761] log likelihood: -4841.978556
EM: Round [762] log likelihood: -4841.978252
EM: Round [763] log likelihood: -4841.977949
EM: Round [764] log likelihood: -4841.977645
EM: Round [765] log likelihood: -4841.977342
EM: Round [766] log likelihood: -4841.977040
EM: Round [767] log likelihood: -4841.976738
EM: Round [768] log likelihood: -4841.976436
EM: Round [769] log likelihood: -4841.976135
EM: Round [770] log likelihood: -4841.975834
EM: Round [771] log likelihood: -4841.975533
EM: Round [772] log likelihood: -4841.975233
EM: Round [773] log likelihood: -4841.974933
EM: Round [774] log likelihood: -4841.974634
EM: Round [775] log likelihood: -4841.974335
EM: Round [776] log likelihood: -4841.974037
EM: Round [777] log likelihood: -4841.973739
EM: Round [778] log likelihood: -4841.973441
EM: Round [779] log likelihood: -4841.973144
EM: Round [780] log likelihood: -4841.972847
EM: Round [781] log likelihood: -4841.972550
EM: Round [782] log likelihood: -4841.972254
EM: Round [783] log likelihood: -4841.971958
EM: Round [784] log likelihood: -4841.971663
EM: Round [785] log likelihood: -4841.971368
EM: Round [786] log likelihood: -4841.971073
EM: Round [787] log likelihood: -4841.970779
EM: Round [788] log likelihood: -4841.970486
EM: Round [789] log likelihood: -4841.970192
EM: Round [790] log likelihood: -4841.969899
EM: Round [791] log likelihood: -4841.969607
EM: Round [792] log likelihood: -4841.969314
EM: Round [793] log likelihood: -4841.969022
EM: Round [794] log likelihood: -4841.968731
EM: Round [795] log likelihood: -4841.968440
EM: Round [796] log likelihood: -4841.968149
EM: Round [797] log likelihood: -4841.967859
EM: Round [798] log likelihood: -4841.967569
EM: Round [799] log likelihood: -4841.967280
EM: Round [800] log likelihood: -4841.966990
EM: Round [801] log likelihood: -4841.966702
EM: Round [802] log likelihood: -4841.966413
EM: Round [803] log likelihood: -4841.966125
EM: Round [804] log likelihood: -4841.965838
EM: Round [805] log likelihood: -4841.965550
EM: Round [806] log likelihood: -4841.965264
EM: Round [807] log likelihood: -4841.964977
EM: Round [808] log likelihood: -4841.964691
EM: Round [809] log likelihood: -4841.964405
EM: Round [810] log likelihood: -4841.964120
EM: Round [811] log likelihood: -4841.963835
EM: Round [812] log likelihood: -4841.963550
EM: Round [813] log likelihood: -4841.963266
EM: Round [814] log likelihood: -4841.962982
EM: Round [815] log likelihood: -4841.962699
EM: Round [816] log likelihood: -4841.962416
EM: Round [817] log likelihood: -4841.962133
EM: Round [818] log likelihood: -4841.961851
EM: Round [819] log likelihood: -4841.961569
EM: Round [820] log likelihood: -4841.961287
EM: Round [821] log likelihood: -4841.961006
EM: Round [822] log likelihood: -4841.960725
EM: Round [823] log likelihood: -4841.960444
EM: Round [824] log likelihood: -4841.960164
EM: Round [825] log likelihood: -4841.959884
EM: Round [826] log likelihood: -4841.959605
EM: Round [827] log likelihood: -4841.959326
EM: Round [828] log likelihood: -4841.959047
EM: Round [829] log likelihood: -4841.958769
EM: Round [830] log likelihood: -4841.958491
EM: Round [831] log likelihood: -4841.958214
EM: Round [832] log likelihood: -4841.957936
EM: Round [833] log likelihood: -4841.957659
EM: Round [834] log likelihood: -4841.957383
EM: Round [835] log likelihood: -4841.957107
EM: Round [836] log likelihood: -4841.956831
EM: Round [837] log likelihood: -4841.956556
EM: Round [838] log likelihood: -4841.956281
EM: Round [839] log likelihood: -4841.956006
EM: Round [840] log likelihood: -4841.955732
EM: Round [841] log likelihood: -4841.955458
EM: Round [842] log likelihood: -4841.955184
EM: Round [843] log likelihood: -4841.954911
EM: Round [844] log likelihood: -4841.954638
EM: Round [845] log likelihood: -4841.954365
EM: Round [846] log likelihood: -4841.954093
EM: Round [847] log likelihood: -4841.953821
EM: Round [848] log likelihood: -4841.953550
EM: Round [849] log likelihood: -4841.953279
EM: Round [850] log likelihood: -4841.953008
EM: Round [851] log likelihood: -4841.952738
EM: Round [852] log likelihood: -4841.952468
EM: Round [853] log likelihood: -4841.952198
EM: Round [854] log likelihood: -4841.951929
EM: Round [855] log likelihood: -4841.951660
EM: Round [856] log likelihood: -4841.951391
EM: Round [857] log likelihood: -4841.951123
EM: Round [858] log likelihood: -4841.950855
EM: Round [859] log likelihood: -4841.950587
EM: Round [860] log likelihood: -4841.950320
EM: Round [861] log likelihood: -4841.950053
EM: Round [862] log likelihood: -4841.949786
EM: Round [863] log likelihood: -4841.949520
EM: Round [864] log likelihood: -4841.949254
EM: Round [865] log likelihood: -4841.948989
EM: Round [866] log likelihood: -4841.948723
EM: Round [867] log likelihood: -4841.948459
EM: Round [868] log likelihood: -4841.948194
EM: Round [869] log likelihood: -4841.947930
EM: Round [870] log likelihood: -4841.947666
EM: Round [871] log likelihood: -4841.947403
EM: Round [872] log likelihood: -4841.947140
EM: Round [873] log likelihood: -4841.946877
EM: Round [874] log likelihood: -4841.946614
EM: Round [875] log likelihood: -4841.946352
EM: Round [876] log likelihood: -4841.946090
EM: Round [877] log likelihood: -4841.945829
EM: Round [878] log likelihood: -4841.945568
EM: Round [879] log likelihood: -4841.945307
EM: Round [880] log likelihood: -4841.945047
EM: Round [881] log likelihood: -4841.944787
EM: Round [882] log likelihood: -4841.944527
EM: Round [883] log likelihood: -4841.944268
EM: Round [884] log likelihood: -4841.944008
EM: Round [885] log likelihood: -4841.943750
EM: Round [886] log likelihood: -4841.943491
EM: Round [887] log likelihood: -4841.943233
EM: Round [888] log likelihood: -4841.942976
EM: Round [889] log likelihood: -4841.942718
EM: Round [890] log likelihood: -4841.942461
EM: Round [891] log likelihood: -4841.942204
EM: Round [892] log likelihood: -4841.941948
EM: Round [893] log likelihood: -4841.941692
EM: Round [894] log likelihood: -4841.941436
EM: Round [895] log likelihood: -4841.941181
EM: Round [896] log likelihood: -4841.940926
EM: Round [897] log likelihood: -4841.940671
EM: Round [898] log likelihood: -4841.940416
EM: Round [899] log likelihood: -4841.940162
EM: Round [900] log likelihood: -4841.939909
EM: Round [901] log likelihood: -4841.939655
EM: Round [902] log likelihood: -4841.939402
EM: Round [903] log likelihood: -4841.939149
EM: Round [904] log likelihood: -4841.938897
EM: Round [905] log likelihood: -4841.938645
EM: Round [906] log likelihood: -4841.938393
EM: Round [907] log likelihood: -4841.938141
EM: Round [908] log likelihood: -4841.937890
EM: Round [909] log likelihood: -4841.937639
EM: Round [910] log likelihood: -4841.937389
EM: Round [911] log likelihood: -4841.937138
EM: Round [912] log likelihood: -4841.936888
EM: Round [913] log likelihood: -4841.936639
EM: Round [914] log likelihood: -4841.936390
EM: Round [915] log likelihood: -4841.936141
EM: Round [916] log likelihood: -4841.935892
EM: Round [917] log likelihood: -4841.935644
EM: Round [918] log likelihood: -4841.935396
EM: Round [919] log likelihood: -4841.935148
EM: Round [920] log likelihood: -4841.934901
EM: Round [921] log likelihood: -4841.934654
EM: Round [922] log likelihood: -4841.934407
EM: Round [923] log likelihood: -4841.934161
EM: Round [924] log likelihood: -4841.933915
EM: Round [925] log likelihood: -4841.933669
EM: Round [926] log likelihood: -4841.933423
EM: Round [927] log likelihood: -4841.933178
EM: Round [928] log likelihood: -4841.932933
EM: Round [929] log likelihood: -4841.932689
EM: Round [930] log likelihood: -4841.932445
EM: Round [931] log likelihood: -4841.932201
EM: Round [932] log likelihood: -4841.931957
EM: Round [933] log likelihood: -4841.931714
EM: Round [934] log likelihood: -4841.931471
EM: Round [935] log likelihood: -4841.931228
EM: Round [936] log likelihood: -4841.930986
EM: Round [937] log likelihood: -4841.930744
EM: Round [938] log likelihood: -4841.930502
EM: Round [939] log likelihood: -4841.930261
EM: Round [940] log likelihood: -4841.930020
EM: Round [941] log likelihood: -4841.929779
EM: Round [942] log likelihood: -4841.929539
EM: Round [943] log likelihood: -4841.929298
EM: Round [944] log likelihood: -4841.929058
EM: Round [945] log likelihood: -4841.928819
EM: Round [946] log likelihood: -4841.928580
EM: Round [947] log likelihood: -4841.928341
EM: Round [948] log likelihood: -4841.928102
EM: Round [949] log likelihood: -4841.927864
EM: Round [950] log likelihood: -4841.927626
EM: Round [951] log likelihood: -4841.927388
EM: Round [952] log likelihood: -4841.927150
EM: Round [953] log likelihood: -4841.926913
EM: Round [954] log likelihood: -4841.926676
EM: Round [955] log likelihood: -4841.926440
EM: Round [956] log likelihood: -4841.926204
EM: Round [957] log likelihood: -4841.925968
EM: Round [958] log likelihood: -4841.925732
EM: Round [959] log likelihood: -4841.925497
EM: Round [960] log likelihood: -4841.925262
EM: Round [961] log likelihood: -4841.925027
EM: Round [962] log likelihood: -4841.924792
EM: Round [963] log likelihood: -4841.924558
EM: Round [964] log likelihood: -4841.924324
EM: Round [965] log likelihood: -4841.924091
EM: Round [966] log likelihood: -4841.923858
EM: Round [967] log likelihood: -4841.923625
EM: Round [968] log likelihood: -4841.923392
EM: Round [969] log likelihood: -4841.923160
EM: Round [970] log likelihood: -4841.922927
EM: Round [971] log likelihood: -4841.922696
EM: Round [972] log likelihood: -4841.922464
EM: Round [973] log likelihood: -4841.922233
EM: Round [974] log likelihood: -4841.922002
EM: Round [975] log likelihood: -4841.921771
EM: Round [976] log likelihood: -4841.921541
EM: Round [977] log likelihood: -4841.921311
EM: Round [978] log likelihood: -4841.921081
EM: Round [979] log likelihood: -4841.920852
EM: Round [980] log likelihood: -4841.920623
EM: Round [981] log likelihood: -4841.920394
EM: Round [982] log likelihood: -4841.920165
EM: Round [983] log likelihood: -4841.919937
EM: Round [984] log likelihood: -4841.919709
EM: Round [985] log likelihood: -4841.919481
EM: Round [986] log likelihood: -4841.919254
EM: Round [987] log likelihood: -4841.919027
EM: Round [988] log likelihood: -4841.918800
EM: Round [989] log likelihood: -4841.918573
EM: Round [990] log likelihood: -4841.918347
EM: Round [991] log likelihood: -4841.918121
EM: Round [992] log likelihood: -4841.917895
EM: Round [993] log likelihood: -4841.917670
EM: Round [994] log likelihood: -4841.917444
EM: Round [995] log likelihood: -4841.917220
EM: Round [996] log likelihood: -4841.916995
EM: Round [997] log likelihood: -4841.916771
EM: Round [998] log likelihood: -4841.916547
EM: Round [999] log likelihood: -4841.916323
EM: Round [1000] log likelihood: -4841.916099
EM: Round [1001] log likelihood: -4841.915876
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz: 295699773
Execution Time = 5.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa --gtf /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fa --gtf /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf > /tmp/nxf.DXIqsdmJjc/fi_workdir/microH.dat
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.DXIqsdmJjc/fi_workdir/microH.dat /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/fi_workdir/microH.dat /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.DXIqsdmJjc --json_outfile /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00628_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.DXIqsdmJjc --json_outfile /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00628_B23MVV7LT4_1
Running: touch /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00628_B23MVV7LT4_1 --html_output /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00628_B23MVV7LT4_1 --html_output /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000251634.2]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.DXIqsdmJjc/ctat_genome_lib_build_dir > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.DXIqsdmJjc/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory