Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/fdfd3a144f13f3a0eadba38f8641d6/tih_rna_sample_00650_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/9c/ce718bf930bc0dc3880e21a9a0c407/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/c7ea523117b40fddc5555c4881c498/tih_rna_sample_00650_B23MVV7LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/ce718bf930bc0dc3880e21a9a0c407/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/fdfd3a144f13f3a0eadba38f8641d6/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00650_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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_00650_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/cytoBand.txt
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00650_B23MVV7LT4_1.star --out_dir /tmp/nxf.HJZ3GQTWH8/fi_workdir --reads "/tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:27:00 ..... started STAR run
Jun 08 10:27:00 ..... loading genome
Jun 08 10:28:50 ... generating Suffix Array index
Jun 08 10:32:57 ... completed Suffix Array index
Jun 08 10:32:57 ..... processing annotations GTF
Jun 08 10:32:57 ..... inserting junctions into the genome indices
Jun 08 10:34:08 ..... started mapping
Jun 08 12:14:44 ..... finished mapping
Jun 08 12:14:47 ..... started sorting BAM
Jun 08 12:14:48 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 107.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00650_B23MVV7LT4_1.star --out_dir /tmp/nxf.HJZ3GQTWH8/fi_workdir --reads "/tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
12:15:06 : INFO : Done.
Execution Time = 0.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[2740000] -done parsing /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 3,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num genes matched < 2' => 306,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 157,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1090,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 138,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 72,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 520,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 135,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
' ** passed ** ' => 15809,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 184,
'low complexity anchor region' => 11,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 78,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 37,
'per_id < 96' => 10646,
'excessive soft clipping' => 16500,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 8,
'small anchor length' => 51,
'seq-similar region overlap' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 42
};
-writing fusion junction support info.
Execution Time = 1.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[17000] -fusion SPANNING read extraction for scaff: CDKN2B--IFNA2
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[207000] -fusion SPANNING read extraction for scaff: IL9RP2--EML4
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[166000] -fusion SPANNING read extraction for scaff: KANK1--LRRK2
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[85000] -fusion SPANNING read extraction for scaff: LRRK2--AHR
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[47000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[57000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[56000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[29000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[25000] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146
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[395000] -fusion SPANNING read extraction for scaff: PTPN2--NPIPB12
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[42000] -fusion SPANNING read extraction for scaff: RITA1--LRRK2
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[26000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[28000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[81000] -fusion SPANNING read extraction for scaff: TUBA4B--SVIL
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[209000] -fusion SPANNING read extraction for scaff: TUBB8--EML4
[1000]
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[31000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 27083,
'seq similar region alignment' => 29889
};
Execution Time = 3.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -12041.010151
EM: Round [1] log likelihood: -12017.738479
EM: Round [2] log likelihood: -12017.403755
EM: Round [3] log likelihood: -12017.343390
EM: Round [4] log likelihood: -12017.316950
EM: Round [5] log likelihood: -12017.301645
EM: Round [6] log likelihood: -12017.290104
EM: Round [7] log likelihood: -12017.279882
EM: Round [8] log likelihood: -12017.270162
EM: Round [9] log likelihood: -12017.260674
EM: Round [10] log likelihood: -12017.251325
EM: Round [11] log likelihood: -12017.242083
EM: Round [12] log likelihood: -12017.232939
EM: Round [13] log likelihood: -12017.223887
EM: Round [14] log likelihood: -12017.214924
EM: Round [15] log likelihood: -12017.206050
EM: Round [16] log likelihood: -12017.197264
EM: Round [17] log likelihood: -12017.188563
EM: Round [18] log likelihood: -12017.179947
EM: Round [19] log likelihood: -12017.171415
EM: Round [20] log likelihood: -12017.162966
EM: Round [21] log likelihood: -12017.154599
EM: Round [22] log likelihood: -12017.146312
EM: Round [23] log likelihood: -12017.138105
EM: Round [24] log likelihood: -12017.129977
EM: Round [25] log likelihood: -12017.121927
EM: Round [26] log likelihood: -12017.113953
EM: Round [27] log likelihood: -12017.106056
EM: Round [28] log likelihood: -12017.098233
EM: Round [29] log likelihood: -12017.090485
EM: Round [30] log likelihood: -12017.082810
EM: Round [31] log likelihood: -12017.075207
EM: Round [32] log likelihood: -12017.067675
EM: Round [33] log likelihood: -12017.060214
EM: Round [34] log likelihood: -12017.052823
EM: Round [35] log likelihood: -12017.045501
EM: Round [36] log likelihood: -12017.038247
EM: Round [37] log likelihood: -12017.031060
EM: Round [38] log likelihood: -12017.023940
EM: Round [39] log likelihood: -12017.016886
EM: Round [40] log likelihood: -12017.009897
EM: Round [41] log likelihood: -12017.002972
EM: Round [42] log likelihood: -12016.996110
EM: Round [43] log likelihood: -12016.989312
EM: Round [44] log likelihood: -12016.982575
EM: Round [45] log likelihood: -12016.975900
EM: Round [46] log likelihood: -12016.969286
EM: Round [47] log likelihood: -12016.962732
EM: Round [48] log likelihood: -12016.956237
EM: Round [49] log likelihood: -12016.949800
EM: Round [50] log likelihood: -12016.943422
EM: Round [51] log likelihood: -12016.937101
EM: Round [52] log likelihood: -12016.930837
EM: Round [53] log likelihood: -12016.924629
EM: Round [54] log likelihood: -12016.918476
EM: Round [55] log likelihood: -12016.912379
EM: Round [56] log likelihood: -12016.906335
EM: Round [57] log likelihood: -12016.900346
EM: Round [58] log likelihood: -12016.894409
EM: Round [59] log likelihood: -12016.888525
EM: Round [60] log likelihood: -12016.882693
EM: Round [61] log likelihood: -12016.876913
EM: Round [62] log likelihood: -12016.871183
EM: Round [63] log likelihood: -12016.865504
EM: Round [64] log likelihood: -12016.859874
EM: Round [65] log likelihood: -12016.854294
EM: Round [66] log likelihood: -12016.848763
EM: Round [67] log likelihood: -12016.843279
EM: Round [68] log likelihood: -12016.837844
EM: Round [69] log likelihood: -12016.832455
EM: Round [70] log likelihood: -12016.827114
EM: Round [71] log likelihood: -12016.821818
EM: Round [72] log likelihood: -12016.816569
EM: Round [73] log likelihood: -12016.811364
EM: Round [74] log likelihood: -12016.806205
EM: Round [75] log likelihood: -12016.801090
EM: Round [76] log likelihood: -12016.796018
EM: Round [77] log likelihood: -12016.790991
EM: Round [78] log likelihood: -12016.786006
EM: Round [79] log likelihood: -12016.781063
EM: Round [80] log likelihood: -12016.776163
EM: Round [81] log likelihood: -12016.771305
EM: Round [82] log likelihood: -12016.766488
EM: Round [83] log likelihood: -12016.761712
EM: Round [84] log likelihood: -12016.756976
EM: Round [85] log likelihood: -12016.752280
EM: Round [86] log likelihood: -12016.747624
EM: Round [87] log likelihood: -12016.743007
EM: Round [88] log likelihood: -12016.738429
EM: Round [89] log likelihood: -12016.733890
EM: Round [90] log likelihood: -12016.729388
EM: Round [91] log likelihood: -12016.724925
EM: Round [92] log likelihood: -12016.720498
EM: Round [93] log likelihood: -12016.716109
EM: Round [94] log likelihood: -12016.711756
EM: Round [95] log likelihood: -12016.707440
EM: Round [96] log likelihood: -12016.703159
EM: Round [97] log likelihood: -12016.698914
EM: Round [98] log likelihood: -12016.694704
EM: Round [99] log likelihood: -12016.690529
EM: Round [100] log likelihood: -12016.686389
EM: Round [101] log likelihood: -12016.682283
EM: Round [102] log likelihood: -12016.678211
EM: Round [103] log likelihood: -12016.674172
EM: Round [104] log likelihood: -12016.670166
EM: Round [105] log likelihood: -12016.666194
EM: Round [106] log likelihood: -12016.662254
EM: Round [107] log likelihood: -12016.658346
EM: Round [108] log likelihood: -12016.654470
EM: Round [109] log likelihood: -12016.650626
EM: Round [110] log likelihood: -12016.646814
EM: Round [111] log likelihood: -12016.643032
EM: Round [112] log likelihood: -12016.639282
EM: Round [113] log likelihood: -12016.635561
EM: Round [114] log likelihood: -12016.631871
EM: Round [115] log likelihood: -12016.628211
EM: Round [116] log likelihood: -12016.624581
EM: Round [117] log likelihood: -12016.620980
EM: Round [118] log likelihood: -12016.617408
EM: Round [119] log likelihood: -12016.613865
EM: Round [120] log likelihood: -12016.610350
EM: Round [121] log likelihood: -12016.606864
EM: Round [122] log likelihood: -12016.603406
EM: Round [123] log likelihood: -12016.599975
EM: Round [124] log likelihood: -12016.596572
EM: Round [125] log likelihood: -12016.593197
EM: Round [126] log likelihood: -12016.589848
EM: Round [127] log likelihood: -12016.586527
EM: Round [128] log likelihood: -12016.583232
EM: Round [129] log likelihood: -12016.579963
EM: Round [130] log likelihood: -12016.576720
EM: Round [131] log likelihood: -12016.573503
EM: Round [132] log likelihood: -12016.570312
EM: Round [133] log likelihood: -12016.567146
EM: Round [134] log likelihood: -12016.564005
EM: Round [135] log likelihood: -12016.560889
EM: Round [136] log likelihood: -12016.557797
EM: Round [137] log likelihood: -12016.554731
EM: Round [138] log likelihood: -12016.551688
EM: Round [139] log likelihood: -12016.548670
EM: Round [140] log likelihood: -12016.545675
EM: Round [141] log likelihood: -12016.542704
EM: Round [142] log likelihood: -12016.539756
EM: Round [143] log likelihood: -12016.536832
EM: Round [144] log likelihood: -12016.533930
EM: Round [145] log likelihood: -12016.531052
EM: Round [146] log likelihood: -12016.528196
EM: Round [147] log likelihood: -12016.525362
EM: Round [148] log likelihood: -12016.522550
EM: Round [149] log likelihood: -12016.519761
EM: Round [150] log likelihood: -12016.516993
EM: Round [151] log likelihood: -12016.514247
EM: Round [152] log likelihood: -12016.511522
EM: Round [153] log likelihood: -12016.508819
EM: Round [154] log likelihood: -12016.506137
EM: Round [155] log likelihood: -12016.503475
EM: Round [156] log likelihood: -12016.500834
EM: Round [157] log likelihood: -12016.498214
EM: Round [158] log likelihood: -12016.495614
EM: Round [159] log likelihood: -12016.493034
EM: Round [160] log likelihood: -12016.490474
EM: Round [161] log likelihood: -12016.487934
EM: Round [162] log likelihood: -12016.485414
EM: Round [163] log likelihood: -12016.482913
EM: Round [164] log likelihood: -12016.480432
EM: Round [165] log likelihood: -12016.477969
EM: Round [166] log likelihood: -12016.475526
EM: Round [167] log likelihood: -12016.473101
EM: Round [168] log likelihood: -12016.470695
EM: Round [169] log likelihood: -12016.468308
EM: Round [170] log likelihood: -12016.465939
EM: Round [171] log likelihood: -12016.463588
EM: Round [172] log likelihood: -12016.461255
EM: Round [173] log likelihood: -12016.458940
EM: Round [174] log likelihood: -12016.456643
EM: Round [175] log likelihood: -12016.454363
EM: Round [176] log likelihood: -12016.452101
EM: Round [177] log likelihood: -12016.449856
EM: Round [178] log likelihood: -12016.447628
EM: Round [179] log likelihood: -12016.445417
EM: Round [180] log likelihood: -12016.443223
EM: Round [181] log likelihood: -12016.441046
EM: Round [182] log likelihood: -12016.438885
EM: Round [183] log likelihood: -12016.436741
EM: Round [184] log likelihood: -12016.434613
EM: Round [185] log likelihood: -12016.432502
EM: Round [186] log likelihood: -12016.430406
EM: Round [187] log likelihood: -12016.428326
EM: Round [188] log likelihood: -12016.426262
EM: Round [189] log likelihood: -12016.424214
EM: Round [190] log likelihood: -12016.422181
EM: Round [191] log likelihood: -12016.420163
EM: Round [192] log likelihood: -12016.418161
EM: Round [193] log likelihood: -12016.416174
EM: Round [194] log likelihood: -12016.414202
EM: Round [195] log likelihood: -12016.412245
EM: Round [196] log likelihood: -12016.410302
EM: Round [197] log likelihood: -12016.408375
EM: Round [198] log likelihood: -12016.406461
EM: Round [199] log likelihood: -12016.404562
EM: Round [200] log likelihood: -12016.402678
EM: Round [201] log likelihood: -12016.400807
EM: Round [202] log likelihood: -12016.398951
EM: Round [203] log likelihood: -12016.397109
EM: Round [204] log likelihood: -12016.395280
EM: Round [205] log likelihood: -12016.393465
EM: Round [206] log likelihood: -12016.391664
EM: Round [207] log likelihood: -12016.389876
EM: Round [208] log likelihood: -12016.388102
EM: Round [209] log likelihood: -12016.386341
EM: Round [210] log likelihood: -12016.384593
EM: Round [211] log likelihood: -12016.382858
EM: Round [212] log likelihood: -12016.381136
EM: Round [213] log likelihood: -12016.379427
EM: Round [214] log likelihood: -12016.377731
EM: Round [215] log likelihood: -12016.376047
EM: Round [216] log likelihood: -12016.374376
EM: Round [217] log likelihood: -12016.372717
EM: Round [218] log likelihood: -12016.371071
EM: Round [219] log likelihood: -12016.369437
EM: Round [220] log likelihood: -12016.367815
EM: Round [221] log likelihood: -12016.366205
EM: Round [222] log likelihood: -12016.364607
EM: Round [223] log likelihood: -12016.363021
EM: Round [224] log likelihood: -12016.361447
EM: Round [225] log likelihood: -12016.359884
EM: Round [226] log likelihood: -12016.358333
EM: Round [227] log likelihood: -12016.356794
EM: Round [228] log likelihood: -12016.355265
EM: Round [229] log likelihood: -12016.353749
EM: Round [230] log likelihood: -12016.352243
EM: Round [231] log likelihood: -12016.350748
EM: Round [232] log likelihood: -12016.349265
EM: Round [233] log likelihood: -12016.347793
EM: Round [234] log likelihood: -12016.346331
EM: Round [235] log likelihood: -12016.344880
EM: Round [236] log likelihood: -12016.343440
EM: Round [237] log likelihood: -12016.342011
EM: Round [238] log likelihood: -12016.340592
EM: Round [239] log likelihood: -12016.339183
EM: Round [240] log likelihood: -12016.337785
EM: Round [241] log likelihood: -12016.336397
EM: Round [242] log likelihood: -12016.335020
EM: Round [243] log likelihood: -12016.333652
EM: Round [244] log likelihood: -12016.332295
EM: Round [245] log likelihood: -12016.330947
EM: Round [246] log likelihood: -12016.329609
EM: Round [247] log likelihood: -12016.328282
EM: Round [248] log likelihood: -12016.326964
EM: Round [249] log likelihood: -12016.325655
EM: Round [250] log likelihood: -12016.324356
EM: Round [251] log likelihood: -12016.323067
EM: Round [252] log likelihood: -12016.321787
EM: Round [253] log likelihood: -12016.320517
EM: Round [254] log likelihood: -12016.319256
EM: Round [255] log likelihood: -12016.318004
EM: Round [256] log likelihood: -12016.316761
EM: Round [257] log likelihood: -12016.315527
EM: Round [258] log likelihood: -12016.314303
EM: Round [259] log likelihood: -12016.313087
EM: Round [260] log likelihood: -12016.311880
EM: Round [261] log likelihood: -12016.310682
EM: Round [262] log likelihood: -12016.309493
EM: Round [263] log likelihood: -12016.308312
EM: Round [264] log likelihood: -12016.307140
EM: Round [265] log likelihood: -12016.305976
EM: Round [266] log likelihood: -12016.304821
EM: Round [267] log likelihood: -12016.303674
EM: Round [268] log likelihood: -12016.302536
EM: Round [269] log likelihood: -12016.301406
EM: Round [270] log likelihood: -12016.300284
EM: Round [271] log likelihood: -12016.299171
EM: Round [272] log likelihood: -12016.298065
EM: Round [273] log likelihood: -12016.296968
EM: Round [274] log likelihood: -12016.295878
EM: Round [275] log likelihood: -12016.294796
EM: Round [276] log likelihood: -12016.293722
EM: Round [277] log likelihood: -12016.292656
EM: Round [278] log likelihood: -12016.291598
EM: Round [279] log likelihood: -12016.290547
EM: Round [280] log likelihood: -12016.289504
EM: Round [281] log likelihood: -12016.288469
EM: Round [282] log likelihood: -12016.287441
EM: Round [283] log likelihood: -12016.286420
EM: Round [284] log likelihood: -12016.285407
EM: Round [285] log likelihood: -12016.284401
EM: Round [286] log likelihood: -12016.283403
EM: Round [287] log likelihood: -12016.282411
EM: Round [288] log likelihood: -12016.281427
EM: Round [289] log likelihood: -12016.280450
EM: Round [290] log likelihood: -12016.279480
EM: Round [291] log likelihood: -12016.278517
EM: Round [292] log likelihood: -12016.277561
EM: Round [293] log likelihood: -12016.276612
EM: Round [294] log likelihood: -12016.275670
EM: Round [295] log likelihood: -12016.274734
EM: Round [296] log likelihood: -12016.273805
EM: Round [297] log likelihood: -12016.272883
EM: Round [298] log likelihood: -12016.271968
EM: Round [299] log likelihood: -12016.271059
EM: Round [300] log likelihood: -12016.270156
EM: Round [301] log likelihood: -12016.269261
EM: Round [302] log likelihood: -12016.268371
EM: Round [303] log likelihood: -12016.267488
EM: Round [304] log likelihood: -12016.266612
EM: Round [305] log likelihood: -12016.265741
EM: Round [306] log likelihood: -12016.264877
EM: Round [307] log likelihood: -12016.264019
EM: Round [308] log likelihood: -12016.263167
EM: Round [309] log likelihood: -12016.262322
EM: Round [310] log likelihood: -12016.261482
EM: Round [311] log likelihood: -12016.260649
EM: Round [312] log likelihood: -12016.259821
EM: Round [313] log likelihood: -12016.259000
EM: Round [314] log likelihood: -12016.258184
EM: Round [315] log likelihood: -12016.257374
EM: Round [316] log likelihood: -12016.256570
EM: Round [317] log likelihood: -12016.255772
EM: Round [318] log likelihood: -12016.254979
EM: Round [319] log likelihood: -12016.254192
EM: Round [320] log likelihood: -12016.253411
EM: Round [321] log likelihood: -12016.252635
EM: Round [322] log likelihood: -12016.251865
EM: Round [323] log likelihood: -12016.251100
EM: Round [324] log likelihood: -12016.250341
EM: Round [325] log likelihood: -12016.249587
EM: Round [326] log likelihood: -12016.248839
EM: Round [327] log likelihood: -12016.248096
EM: Round [328] log likelihood: -12016.247358
EM: Round [329] log likelihood: -12016.246626
EM: Round [330] log likelihood: -12016.245898
EM: Round [331] log likelihood: -12016.245176
EM: Round [332] log likelihood: -12016.244459
EM: Round [333] log likelihood: -12016.243748
EM: Round [334] log likelihood: -12016.243041
EM: Round [335] log likelihood: -12016.242339
EM: Round [336] log likelihood: -12016.241643
EM: Round [337] log likelihood: -12016.240951
EM: Round [338] log likelihood: -12016.240264
EM: Round [339] log likelihood: -12016.239582
EM: Round [340] log likelihood: -12016.238905
EM: Round [341] log likelihood: -12016.238233
EM: Round [342] log likelihood: -12016.237566
EM: Round [343] log likelihood: -12016.236903
EM: Round [344] log likelihood: -12016.236245
EM: Round [345] log likelihood: -12016.235592
EM: Round [346] log likelihood: -12016.234943
EM: Round [347] log likelihood: -12016.234299
EM: Round [348] log likelihood: -12016.233660
EM: Round [349] log likelihood: -12016.233025
EM: Round [350] log likelihood: -12016.232395
EM: Round [351] log likelihood: -12016.231769
EM: Round [352] log likelihood: -12016.231147
EM: Round [353] log likelihood: -12016.230530
EM: Round [354] log likelihood: -12016.229918
EM: Round [355] log likelihood: -12016.229309
EM: Round [356] log likelihood: -12016.228705
EM: Round [357] log likelihood: -12016.228106
EM: Round [358] log likelihood: -12016.227510
EM: Round [359] log likelihood: -12016.226919
EM: Round [360] log likelihood: -12016.226332
EM: Round [361] log likelihood: -12016.225749
EM: Round [362] log likelihood: -12016.225171
EM: Round [363] log likelihood: -12016.224596
EM: Round [364] log likelihood: -12016.224025
EM: Round [365] log likelihood: -12016.223459
EM: Round [366] log likelihood: -12016.222896
EM: Round [367] log likelihood: -12016.222338
EM: Round [368] log likelihood: -12016.221783
EM: Round [369] log likelihood: -12016.221233
EM: Round [370] log likelihood: -12016.220686
EM: Round [371] log likelihood: -12016.220143
EM: Round [372] log likelihood: -12016.219604
EM: Round [373] log likelihood: -12016.219069
EM: Round [374] log likelihood: -12016.218538
EM: Round [375] log likelihood: -12016.218010
EM: Round [376] log likelihood: -12016.217486
EM: Round [377] log likelihood: -12016.216966
EM: Round [378] log likelihood: -12016.216449
EM: Round [379] log likelihood: -12016.215936
EM: Round [380] log likelihood: -12016.215427
EM: Round [381] log likelihood: -12016.214921
EM: Round [382] log likelihood: -12016.214419
EM: Round [383] log likelihood: -12016.213921
EM: Round [384] log likelihood: -12016.213426
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EM: Round [386] log likelihood: -12016.212446
EM: Round [387] log likelihood: -12016.211961
EM: Round [388] log likelihood: -12016.211480
EM: Round [389] log likelihood: -12016.211002
EM: Round [390] log likelihood: -12016.210528
EM: Round [391] log likelihood: -12016.210057
EM: Round [392] log likelihood: -12016.209589
EM: Round [393] log likelihood: -12016.209125
EM: Round [394] log likelihood: -12016.208664
EM: Round [395] log likelihood: -12016.208206
EM: Round [396] log likelihood: -12016.207751
EM: Round [397] log likelihood: -12016.207299
EM: Round [398] log likelihood: -12016.206851
EM: Round [399] log likelihood: -12016.206406
EM: Round [400] log likelihood: -12016.205964
EM: Round [401] log likelihood: -12016.205525
EM: Round [402] log likelihood: -12016.205089
EM: Round [403] log likelihood: -12016.204656
EM: Round [404] log likelihood: -12016.204227
EM: Round [405] log likelihood: -12016.203800
EM: Round [406] log likelihood: -12016.203376
EM: Round [407] log likelihood: -12016.202956
EM: Round [408] log likelihood: -12016.202538
EM: Round [409] log likelihood: -12016.202123
EM: Round [410] log likelihood: -12016.201711
EM: Round [411] log likelihood: -12016.201302
EM: Round [412] log likelihood: -12016.200896
EM: Round [413] log likelihood: -12016.200493
EM: Round [414] log likelihood: -12016.200092
EM: Round [415] log likelihood: -12016.199695
EM: Round [416] log likelihood: -12016.199300
EM: Round [417] log likelihood: -12016.198908
EM: Round [418] log likelihood: -12016.198519
EM: Round [419] log likelihood: -12016.198132
EM: Round [420] log likelihood: -12016.197748
EM: Round [421] log likelihood: -12016.197367
EM: Round [422] log likelihood: -12016.196989
EM: Round [423] log likelihood: -12016.196613
EM: Round [424] log likelihood: -12016.196240
EM: Round [425] log likelihood: -12016.195869
EM: Round [426] log likelihood: -12016.195501
EM: Round [427] log likelihood: -12016.195136
EM: Round [428] log likelihood: -12016.194773
EM: Round [429] log likelihood: -12016.194413
EM: Round [430] log likelihood: -12016.194055
EM: Round [431] log likelihood: -12016.193700
EM: Round [432] log likelihood: -12016.193347
EM: Round [433] log likelihood: -12016.192997
EM: Round [434] log likelihood: -12016.192649
EM: Round [435] log likelihood: -12016.192304
EM: Round [436] log likelihood: -12016.191961
EM: Round [437] log likelihood: -12016.191620
EM: Round [438] log likelihood: -12016.191282
EM: Round [439] log likelihood: -12016.190946
EM: Round [440] log likelihood: -12016.190613
EM: Round [441] log likelihood: -12016.190282
EM: Round [442] log likelihood: -12016.189953
EM: Round [443] log likelihood: -12016.189627
EM: Round [444] log likelihood: -12016.189302
EM: Round [445] log likelihood: -12016.188981
EM: Round [446] log likelihood: -12016.188661
EM: Round [447] log likelihood: -12016.188343
EM: Round [448] log likelihood: -12016.188028
EM: Round [449] log likelihood: -12016.187715
EM: Round [450] log likelihood: -12016.187405
EM: Round [451] log likelihood: -12016.187096
EM: Round [452] log likelihood: -12016.186789
EM: Round [453] log likelihood: -12016.186485
EM: Round [454] log likelihood: -12016.186183
EM: Round [455] log likelihood: -12016.185883
EM: Round [456] log likelihood: -12016.185585
EM: Round [457] log likelihood: -12016.185289
EM: Round [458] log likelihood: -12016.184995
EM: Round [459] log likelihood: -12016.184703
EM: Round [460] log likelihood: -12016.184414
EM: Round [461] log likelihood: -12016.184126
EM: Round [462] log likelihood: -12016.183840
EM: Round [463] log likelihood: -12016.183557
EM: Round [464] log likelihood: -12016.183275
EM: Round [465] log likelihood: -12016.182995
EM: Round [466] log likelihood: -12016.182718
EM: Round [467] log likelihood: -12016.182442
EM: Round [468] log likelihood: -12016.182168
EM: Round [469] log likelihood: -12016.181896
EM: Round [470] log likelihood: -12016.181626
EM: Round [471] log likelihood: -12016.181358
EM: Round [472] log likelihood: -12016.181091
EM: Round [473] log likelihood: -12016.180827
EM: Round [474] log likelihood: -12016.180564
EM: Round [475] log likelihood: -12016.180303
EM: Round [476] log likelihood: -12016.180044
EM: Round [477] log likelihood: -12016.179787
EM: Round [478] log likelihood: -12016.179532
EM: Round [479] log likelihood: -12016.179278
EM: Round [480] log likelihood: -12016.179026
EM: Round [481] log likelihood: -12016.178776
EM: Round [482] log likelihood: -12016.178528
EM: Round [483] log likelihood: -12016.178282
EM: Round [484] log likelihood: -12016.178037
EM: Round [485] log likelihood: -12016.177794
EM: Round [486] log likelihood: -12016.177552
EM: Round [487] log likelihood: -12016.177312
EM: Round [488] log likelihood: -12016.177074
EM: Round [489] log likelihood: -12016.176838
EM: Round [490] log likelihood: -12016.176603
EM: Round [491] log likelihood: -12016.176370
EM: Round [492] log likelihood: -12016.176138
EM: Round [493] log likelihood: -12016.175908
EM: Round [494] log likelihood: -12016.175680
EM: Round [495] log likelihood: -12016.175453
EM: Round [496] log likelihood: -12016.175228
EM: Round [497] log likelihood: -12016.175005
EM: Round [498] log likelihood: -12016.174783
EM: Round [499] log likelihood: -12016.174562
EM: Round [500] log likelihood: -12016.174343
EM: Round [501] log likelihood: -12016.174126
EM: Round [502] log likelihood: -12016.173910
EM: Round [503] log likelihood: -12016.173696
EM: Round [504] log likelihood: -12016.173483
EM: Round [505] log likelihood: -12016.173272
EM: Round [506] log likelihood: -12016.173062
EM: Round [507] log likelihood: -12016.172853
EM: Round [508] log likelihood: -12016.172646
EM: Round [509] log likelihood: -12016.172441
EM: Round [510] log likelihood: -12016.172236
EM: Round [511] log likelihood: -12016.172034
EM: Round [512] log likelihood: -12016.171832
EM: Round [513] log likelihood: -12016.171633
EM: Round [514] log likelihood: -12016.171434
EM: Round [515] log likelihood: -12016.171237
EM: Round [516] log likelihood: -12016.171041
EM: Round [517] log likelihood: -12016.170847
EM: Round [518] log likelihood: -12016.170654
EM: Round [519] log likelihood: -12016.170462
EM: Round [520] log likelihood: -12016.170272
EM: Round [521] log likelihood: -12016.170083
EM: Round [522] log likelihood: -12016.169895
EM: Round [523] log likelihood: -12016.169709
EM: Round [524] log likelihood: -12016.169523
EM: Round [525] log likelihood: -12016.169340
EM: Round [526] log likelihood: -12016.169157
EM: Round [527] log likelihood: -12016.168976
EM: Round [528] log likelihood: -12016.168796
EM: Round [529] log likelihood: -12016.168617
EM: Round [530] log likelihood: -12016.168440
EM: Round [531] log likelihood: -12016.168263
EM: Round [532] log likelihood: -12016.168088
EM: Round [533] log likelihood: -12016.167914
EM: Round [534] log likelihood: -12016.167742
EM: Round [535] log likelihood: -12016.167570
EM: Round [536] log likelihood: -12016.167400
EM: Round [537] log likelihood: -12016.167231
EM: Round [538] log likelihood: -12016.167063
EM: Round [539] log likelihood: -12016.166896
EM: Round [540] log likelihood: -12016.166731
EM: Round [541] log likelihood: -12016.166567
EM: Round [542] log likelihood: -12016.166403
EM: Round [543] log likelihood: -12016.166241
EM: Round [544] log likelihood: -12016.166080
EM: Round [545] log likelihood: -12016.165920
EM: Round [546] log likelihood: -12016.165762
EM: Round [547] log likelihood: -12016.165604
EM: Round [548] log likelihood: -12016.165447
EM: Round [549] log likelihood: -12016.165292
EM: Round [550] log likelihood: -12016.165137
EM: Round [551] log likelihood: -12016.164984
EM: Round [552] log likelihood: -12016.164832
EM: Round [553] log likelihood: -12016.164681
EM: Round [554] log likelihood: -12016.164530
EM: Round [555] log likelihood: -12016.164381
EM: Round [556] log likelihood: -12016.164233
EM: Round [557] log likelihood: -12016.164086
EM: Round [558] log likelihood: -12016.163940
EM: Round [559] log likelihood: -12016.163795
EM: Round [560] log likelihood: -12016.163651
EM: Round [561] log likelihood: -12016.163508
EM: Round [562] log likelihood: -12016.163366
EM: Round [563] log likelihood: -12016.163225
EM: Round [564] log likelihood: -12016.163085
EM: Round [565] log likelihood: -12016.162946
EM: Round [566] log likelihood: -12016.162808
EM: Round [567] log likelihood: -12016.162671
EM: Round [568] log likelihood: -12016.162535
EM: Round [569] log likelihood: -12016.162399
EM: Round [570] log likelihood: -12016.162265
EM: Round [571] log likelihood: -12016.162132
EM: Round [572] log likelihood: -12016.161999
EM: Round [573] log likelihood: -12016.161868
EM: Round [574] log likelihood: -12016.161737
EM: Round [575] log likelihood: -12016.161607
EM: Round [576] log likelihood: -12016.161479
EM: Round [577] log likelihood: -12016.161351
EM: Round [578] log likelihood: -12016.161224
EM: Round [579] log likelihood: -12016.161097
EM: Round [580] log likelihood: -12016.160972
EM: Round [581] log likelihood: -12016.160848
EM: Round [582] log likelihood: -12016.160724
EM: Round [583] log likelihood: -12016.160602
EM: Round [584] log likelihood: -12016.160480
EM: Round [585] log likelihood: -12016.160359
EM: Round [586] log likelihood: -12016.160239
EM: Round [587] log likelihood: -12016.160119
EM: Round [588] log likelihood: -12016.160001
EM: Round [589] log likelihood: -12016.159883
EM: Round [590] log likelihood: -12016.159766
EM: Round [591] log likelihood: -12016.159650
EM: Round [592] log likelihood: -12016.159535
EM: Round [593] log likelihood: -12016.159421
EM: Round [594] log likelihood: -12016.159307
EM: Round [595] log likelihood: -12016.159194
EM: Round [596] log likelihood: -12016.159082
EM: Round [597] log likelihood: -12016.158971
EM: Round [598] log likelihood: -12016.158860
EM: Round [599] log likelihood: -12016.158750
EM: Round [600] log likelihood: -12016.158641
EM: Round [601] log likelihood: -12016.158533
EM: Round [602] log likelihood: -12016.158426
EM: Round [603] log likelihood: -12016.158319
EM: Round [604] log likelihood: -12016.158213
EM: Round [605] log likelihood: -12016.158108
EM: Round [606] log likelihood: -12016.158003
EM: Round [607] log likelihood: -12016.157899
EM: Round [608] log likelihood: -12016.157796
EM: Round [609] log likelihood: -12016.157694
EM: Round [610] log likelihood: -12016.157592
EM: Round [611] log likelihood: -12016.157491
EM: Round [612] log likelihood: -12016.157391
EM: Round [613] log likelihood: -12016.157291
EM: Stopping iterations at round 613 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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir
-done, see /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -11533.090684
EM: Round [1] log likelihood: -11532.630869
EM: Round [2] log likelihood: -11532.630623
EM: Round [3] log likelihood: -11532.630622
EM: Stopping iterations at round 3 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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz: 296362499
Execution Time = 5.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa --gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa --gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/fi_workdir/microH.dat
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.HJZ3GQTWH8/fi_workdir/microH.dat /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/fi_workdir/microH.dat /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HJZ3GQTWH8 --json_outfile /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00650_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.HJZ3GQTWH8 --json_outfile /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00650_B23MVV7LT4_1
Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00650_B23MVV7LT4_1 --html_output /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00650_B23MVV7LT4_1 --html_output /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
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 [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory