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/cb/e4849de20220debe757fa3abdb1467/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e4849de20220debe757fa3abdb1467/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/5f1b58950886125572f51223428af3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e81a6ca03cf9d7ef81a56126a150b0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e81a6ca03cf9d7ef81a56126a150b0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/cytoBand.txt
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fqPNrqQpK0/fi_workdir --reads "/tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 11:09:55 ..... started STAR run
Jun 08 11:09:55 ..... loading genome
Jun 08 11:11:35 ... generating Suffix Array index
Jun 08 11:15:13 ... completed Suffix Array index
Jun 08 11:15:14 ..... processing annotations GTF
Jun 08 11:15:14 ..... inserting junctions into the genome indices
Jun 08 11:16:14 ..... started mapping
Jun 08 12:08:01 ..... finished mapping
Jun 08 12:08:02 ..... started sorting BAM
Jun 08 12:08:03 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 58.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fqPNrqQpK0/fi_workdir --reads "/tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
12:08:18 : INFO : Done.
Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[2650000] -done parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 71,
'per_id < 96' => 23779,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 110,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'small anchor length' => 191,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'seq-similar region overlap' => 398,
' ** passed ** ' => 25067,
'num genes matched < 2' => 64,
'excessive soft clipping' => 18690,
'low complexity anchor region' => 22,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 402,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4
};
-writing fusion junction support info.
Execution Time = 1.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[392000] -fusion SPANNING read extraction for scaff: CPSF6--DUX4
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[245000] -fusion SPANNING read extraction for scaff: EPC1--PHC2
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[165000] -fusion SPANNING read extraction for scaff: EPC1--TLR12P
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[151000] -fusion SPANNING read extraction for scaff: FBXO10--SETD2
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[27000] -fusion SPANNING read extraction for scaff: FP325317.1--BMS1P10
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[43000] -fusion SPANNING read extraction for scaff: FXYD1--FXYD5
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[56000] -fusion SPANNING read extraction for scaff: KDM4C--ZCCHC7
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[85000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[21000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[11000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[49000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[12000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[18000] -fusion SPANNING read extraction for scaff: ZCCHC7--AL513412.1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 121957,
'lacks exon overlap' => 6159
};
Execution Time = 3.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7880.709345
EM: Round [1] log likelihood: -7875.243300
EM: Round [2] log likelihood: -7872.563037
EM: Round [3] log likelihood: -7870.373075
EM: Round [4] log likelihood: -7868.569623
EM: Round [5] log likelihood: -7867.074523
EM: Round [6] log likelihood: -7865.827336
EM: Round [7] log likelihood: -7864.780710
EM: Round [8] log likelihood: -7863.897176
EM: Round [9] log likelihood: -7863.146856
EM: Round [10] log likelihood: -7862.505778
EM: Round [11] log likelihood: -7861.954612
EM: Round [12] log likelihood: -7861.477710
EM: Round [13] log likelihood: -7861.062359
EM: Round [14] log likelihood: -7860.698200
EM: Round [15] log likelihood: -7860.376773
EM: Round [16] log likelihood: -7860.091149
EM: Round [17] log likelihood: -7859.835643
EM: Round [18] log likelihood: -7859.605579
EM: Round [19] log likelihood: -7859.397105
EM: Round [20] log likelihood: -7859.207039
EM: Round [21] log likelihood: -7859.032748
EM: Round [22] log likelihood: -7858.872046
EM: Round [23] log likelihood: -7858.723118
EM: Round [24] log likelihood: -7858.584447
EM: Round [25] log likelihood: -7858.454766
EM: Round [26] log likelihood: -7858.333011
EM: Round [27] log likelihood: -7858.218286
EM: Round [28] log likelihood: -7858.109835
EM: Round [29] log likelihood: -7858.007013
EM: Round [30] log likelihood: -7857.909273
EM: Round [31] log likelihood: -7857.816145
EM: Round [32] log likelihood: -7857.727223
EM: Round [33] log likelihood: -7857.642158
EM: Round [34] log likelihood: -7857.560645
EM: Round [35] log likelihood: -7857.482416
EM: Round [36] log likelihood: -7857.407235
EM: Round [37] log likelihood: -7857.334894
EM: Round [38] log likelihood: -7857.265207
EM: Round [39] log likelihood: -7857.198008
EM: Round [40] log likelihood: -7857.133147
EM: Round [41] log likelihood: -7857.070486
EM: Round [42] log likelihood: -7857.009903
EM: Round [43] log likelihood: -7856.951284
EM: Round [44] log likelihood: -7856.894524
EM: Round [45] log likelihood: -7856.839529
EM: Round [46] log likelihood: -7856.786207
EM: Round [47] log likelihood: -7856.734477
EM: Round [48] log likelihood: -7856.684262
EM: Round [49] log likelihood: -7856.635488
EM: Round [50] log likelihood: -7856.588090
EM: Round [51] log likelihood: -7856.542003
EM: Round [52] log likelihood: -7856.497167
EM: Round [53] log likelihood: -7856.453527
EM: Round [54] log likelihood: -7856.411029
EM: Round [55] log likelihood: -7856.369623
EM: Round [56] log likelihood: -7856.329262
EM: Round [57] log likelihood: -7856.289900
EM: Round [58] log likelihood: -7856.251496
EM: Round [59] log likelihood: -7856.214009
EM: Round [60] log likelihood: -7856.177400
EM: Round [61] log likelihood: -7856.141634
EM: Round [62] log likelihood: -7856.106675
EM: Round [63] log likelihood: -7856.072492
EM: Round [64] log likelihood: -7856.039053
EM: Round [65] log likelihood: -7856.006328
EM: Round [66] log likelihood: -7855.974290
EM: Round [67] log likelihood: -7855.942911
EM: Round [68] log likelihood: -7855.912166
EM: Round [69] log likelihood: -7855.882031
EM: Round [70] log likelihood: -7855.852484
EM: Round [71] log likelihood: -7855.823501
EM: Round [72] log likelihood: -7855.795062
EM: Round [73] log likelihood: -7855.767147
EM: Round [74] log likelihood: -7855.739738
EM: Round [75] log likelihood: -7855.712816
EM: Round [76] log likelihood: -7855.686365
EM: Round [77] log likelihood: -7855.660367
EM: Round [78] log likelihood: -7855.634807
EM: Round [79] log likelihood: -7855.609671
EM: Round [80] log likelihood: -7855.584944
EM: Round [81] log likelihood: -7855.560612
EM: Round [82] log likelihood: -7855.536664
EM: Round [83] log likelihood: -7855.513086
EM: Round [84] log likelihood: -7855.489867
EM: Round [85] log likelihood: -7855.466996
EM: Round [86] log likelihood: -7855.444462
EM: Round [87] log likelihood: -7855.422254
EM: Round [88] log likelihood: -7855.400364
EM: Round [89] log likelihood: -7855.378782
EM: Round [90] log likelihood: -7855.357499
EM: Round [91] log likelihood: -7855.336506
EM: Round [92] log likelihood: -7855.315795
EM: Round [93] log likelihood: -7855.295359
EM: Round [94] log likelihood: -7855.275191
EM: Round [95] log likelihood: -7855.255282
EM: Round [96] log likelihood: -7855.235627
EM: Round [97] log likelihood: -7855.216218
EM: Round [98] log likelihood: -7855.197050
EM: Round [99] log likelihood: -7855.178117
EM: Round [100] log likelihood: -7855.159412
EM: Round [101] log likelihood: -7855.140931
EM: Round [102] log likelihood: -7855.122667
EM: Round [103] log likelihood: -7855.104617
EM: Round [104] log likelihood: -7855.086775
EM: Round [105] log likelihood: -7855.069136
EM: Round [106] log likelihood: -7855.051696
EM: Round [107] log likelihood: -7855.034450
EM: Round [108] log likelihood: -7855.017395
EM: Round [109] log likelihood: -7855.000527
EM: Round [110] log likelihood: -7854.983841
EM: Round [111] log likelihood: -7854.967334
EM: Round [112] log likelihood: -7854.951002
EM: Round [113] log likelihood: -7854.934842
EM: Round [114] log likelihood: -7854.918850
EM: Round [115] log likelihood: -7854.903024
EM: Round [116] log likelihood: -7854.887360
EM: Round [117] log likelihood: -7854.871855
EM: Round [118] log likelihood: -7854.856506
EM: Round [119] log likelihood: -7854.841311
EM: Round [120] log likelihood: -7854.826267
EM: Round [121] log likelihood: -7854.811370
EM: Round [122] log likelihood: -7854.796619
EM: Round [123] log likelihood: -7854.782012
EM: Round [124] log likelihood: -7854.767545
EM: Round [125] log likelihood: -7854.753216
EM: Round [126] log likelihood: -7854.739024
EM: Round [127] log likelihood: -7854.724966
EM: Round [128] log likelihood: -7854.711039
EM: Round [129] log likelihood: -7854.697243
EM: Round [130] log likelihood: -7854.683574
EM: Round [131] log likelihood: -7854.670031
EM: Round [132] log likelihood: -7854.656612
EM: Round [133] log likelihood: -7854.643315
EM: Round [134] log likelihood: -7854.630138
EM: Round [135] log likelihood: -7854.617081
EM: Round [136] log likelihood: -7854.604140
EM: Round [137] log likelihood: -7854.591314
EM: Round [138] log likelihood: -7854.578602
EM: Round [139] log likelihood: -7854.566002
EM: Round [140] log likelihood: -7854.553513
EM: Round [141] log likelihood: -7854.541132
EM: Round [142] log likelihood: -7854.528859
EM: Round [143] log likelihood: -7854.516693
EM: Round [144] log likelihood: -7854.504631
EM: Round [145] log likelihood: -7854.492672
EM: Round [146] log likelihood: -7854.480816
EM: Round [147] log likelihood: -7854.469060
EM: Round [148] log likelihood: -7854.457403
EM: Round [149] log likelihood: -7854.445845
EM: Round [150] log likelihood: -7854.434384
EM: Round [151] log likelihood: -7854.423019
EM: Round [152] log likelihood: -7854.411748
EM: Round [153] log likelihood: -7854.400571
EM: Round [154] log likelihood: -7854.389486
EM: Round [155] log likelihood: -7854.378492
EM: Round [156] log likelihood: -7854.367588
EM: Round [157] log likelihood: -7854.356774
EM: Round [158] log likelihood: -7854.346047
EM: Round [159] log likelihood: -7854.335408
EM: Round [160] log likelihood: -7854.324854
EM: Round [161] log likelihood: -7854.314386
EM: Round [162] log likelihood: -7854.304001
EM: Round [163] log likelihood: -7854.293700
EM: Round [164] log likelihood: -7854.283481
EM: Round [165] log likelihood: -7854.273343
EM: Round [166] log likelihood: -7854.263285
EM: Round [167] log likelihood: -7854.253307
EM: Round [168] log likelihood: -7854.243408
EM: Round [169] log likelihood: -7854.233586
EM: Round [170] log likelihood: -7854.223841
EM: Round [171] log likelihood: -7854.214172
EM: Round [172] log likelihood: -7854.204579
EM: Round [173] log likelihood: -7854.195060
EM: Round [174] log likelihood: -7854.185614
EM: Round [175] log likelihood: -7854.176241
EM: Round [176] log likelihood: -7854.166941
EM: Round [177] log likelihood: -7854.157712
EM: Round [178] log likelihood: -7854.148553
EM: Round [179] log likelihood: -7854.139465
EM: Round [180] log likelihood: -7854.130445
EM: Round [181] log likelihood: -7854.121494
EM: Round [182] log likelihood: -7854.112611
EM: Round [183] log likelihood: -7854.103795
EM: Round [184] log likelihood: -7854.095045
EM: Round [185] log likelihood: -7854.086361
EM: Round [186] log likelihood: -7854.077742
EM: Round [187] log likelihood: -7854.069188
EM: Round [188] log likelihood: -7854.060697
EM: Round [189] log likelihood: -7854.052269
EM: Round [190] log likelihood: -7854.043904
EM: Round [191] log likelihood: -7854.035601
EM: Round [192] log likelihood: -7854.027359
EM: Round [193] log likelihood: -7854.019178
EM: Round [194] log likelihood: -7854.011058
EM: Round [195] log likelihood: -7854.002996
EM: Round [196] log likelihood: -7853.994994
EM: Round [197] log likelihood: -7853.987050
EM: Round [198] log likelihood: -7853.979164
EM: Round [199] log likelihood: -7853.971335
EM: Round [200] log likelihood: -7853.963563
EM: Round [201] log likelihood: -7853.955848
EM: Round [202] log likelihood: -7853.948188
EM: Round [203] log likelihood: -7853.940583
EM: Round [204] log likelihood: -7853.933033
EM: Round [205] log likelihood: -7853.925537
EM: Round [206] log likelihood: -7853.918095
EM: Round [207] log likelihood: -7853.910706
EM: Round [208] log likelihood: -7853.903370
EM: Round [209] log likelihood: -7853.896086
EM: Round [210] log likelihood: -7853.888853
EM: Round [211] log likelihood: -7853.881672
EM: Round [212] log likelihood: -7853.874542
EM: Round [213] log likelihood: -7853.867462
EM: Round [214] log likelihood: -7853.860432
EM: Round [215] log likelihood: -7853.853452
EM: Round [216] log likelihood: -7853.846520
EM: Round [217] log likelihood: -7853.839637
EM: Round [218] log likelihood: -7853.832802
EM: Round [219] log likelihood: -7853.826015
EM: Round [220] log likelihood: -7853.819275
EM: Round [221] log likelihood: -7853.812582
EM: Round [222] log likelihood: -7853.805936
EM: Round [223] log likelihood: -7853.799336
EM: Round [224] log likelihood: -7853.792781
EM: Round [225] log likelihood: -7853.786271
EM: Round [226] log likelihood: -7853.779807
EM: Round [227] log likelihood: -7853.773386
EM: Round [228] log likelihood: -7853.767010
EM: Round [229] log likelihood: -7853.760678
EM: Round [230] log likelihood: -7853.754389
EM: Round [231] log likelihood: -7853.748143
EM: Round [232] log likelihood: -7853.741940
EM: Round [233] log likelihood: -7853.735778
EM: Round [234] log likelihood: -7853.729659
EM: Round [235] log likelihood: -7853.723581
EM: Round [236] log likelihood: -7853.717545
EM: Round [237] log likelihood: -7853.711549
EM: Round [238] log likelihood: -7853.705594
EM: Round [239] log likelihood: -7853.699679
EM: Round [240] log likelihood: -7853.693803
EM: Round [241] log likelihood: -7853.687968
EM: Round [242] log likelihood: -7853.682171
EM: Round [243] log likelihood: -7853.676413
EM: Round [244] log likelihood: -7853.670694
EM: Round [245] log likelihood: -7853.665013
EM: Round [246] log likelihood: -7853.659370
EM: Round [247] log likelihood: -7853.653764
EM: Round [248] log likelihood: -7853.648196
EM: Round [249] log likelihood: -7853.642665
EM: Round [250] log likelihood: -7853.637170
EM: Round [251] log likelihood: -7853.631712
EM: Round [252] log likelihood: -7853.626290
EM: Round [253] log likelihood: -7853.620903
EM: Round [254] log likelihood: -7853.615552
EM: Round [255] log likelihood: -7853.610237
EM: Round [256] log likelihood: -7853.604956
EM: Round [257] log likelihood: -7853.599710
EM: Round [258] log likelihood: -7853.594498
EM: Round [259] log likelihood: -7853.589321
EM: Round [260] log likelihood: -7853.584177
EM: Round [261] log likelihood: -7853.579067
EM: Round [262] log likelihood: -7853.573990
EM: Round [263] log likelihood: -7853.568946
EM: Round [264] log likelihood: -7853.563935
EM: Round [265] log likelihood: -7853.558956
EM: Round [266] log likelihood: -7853.554010
EM: Round [267] log likelihood: -7853.549096
EM: Round [268] log likelihood: -7853.544213
EM: Round [269] log likelihood: -7853.539362
EM: Round [270] log likelihood: -7853.534543
EM: Round [271] log likelihood: -7853.529754
EM: Round [272] log likelihood: -7853.524996
EM: Round [273] log likelihood: -7853.520269
EM: Round [274] log likelihood: -7853.515572
EM: Round [275] log likelihood: -7853.510905
EM: Round [276] log likelihood: -7853.506268
EM: Round [277] log likelihood: -7853.501661
EM: Round [278] log likelihood: -7853.497083
EM: Round [279] log likelihood: -7853.492534
EM: Round [280] log likelihood: -7853.488014
EM: Round [281] log likelihood: -7853.483523
EM: Round [282] log likelihood: -7853.479061
EM: Round [283] log likelihood: -7853.474627
EM: Round [284] log likelihood: -7853.470220
EM: Round [285] log likelihood: -7853.465842
EM: Round [286] log likelihood: -7853.461492
EM: Round [287] log likelihood: -7853.457169
EM: Round [288] log likelihood: -7853.452873
EM: Round [289] log likelihood: -7853.448604
EM: Round [290] log likelihood: -7853.444362
EM: Round [291] log likelihood: -7853.440147
EM: Round [292] log likelihood: -7853.435958
EM: Round [293] log likelihood: -7853.431796
EM: Round [294] log likelihood: -7853.427660
EM: Round [295] log likelihood: -7853.423549
EM: Round [296] log likelihood: -7853.419464
EM: Round [297] log likelihood: -7853.415405
EM: Round [298] log likelihood: -7853.411371
EM: Round [299] log likelihood: -7853.407362
EM: Round [300] log likelihood: -7853.403378
EM: Round [301] log likelihood: -7853.399419
EM: Round [302] log likelihood: -7853.395485
EM: Round [303] log likelihood: -7853.391575
EM: Round [304] log likelihood: -7853.387689
EM: Round [305] log likelihood: -7853.383827
EM: Round [306] log likelihood: -7853.379989
EM: Round [307] log likelihood: -7853.376175
EM: Round [308] log likelihood: -7853.372384
EM: Round [309] log likelihood: -7853.368617
EM: Round [310] log likelihood: -7853.364873
EM: Round [311] log likelihood: -7853.361152
EM: Round [312] log likelihood: -7853.357454
EM: Round [313] log likelihood: -7853.353778
EM: Round [314] log likelihood: -7853.350126
EM: Round [315] log likelihood: -7853.346495
EM: Round [316] log likelihood: -7853.342887
EM: Round [317] log likelihood: -7853.339301
EM: Round [318] log likelihood: -7853.335736
EM: Round [319] log likelihood: -7853.332194
EM: Round [320] log likelihood: -7853.328673
EM: Round [321] log likelihood: -7853.325174
EM: Round [322] log likelihood: -7853.321696
EM: Round [323] log likelihood: -7853.318239
EM: Round [324] log likelihood: -7853.314803
EM: Round [325] log likelihood: -7853.311388
EM: Round [326] log likelihood: -7853.307993
EM: Round [327] log likelihood: -7853.304620
EM: Round [328] log likelihood: -7853.301266
EM: Round [329] log likelihood: -7853.297933
EM: Round [330] log likelihood: -7853.294620
EM: Round [331] log likelihood: -7853.291327
EM: Round [332] log likelihood: -7853.288054
EM: Round [333] log likelihood: -7853.284801
EM: Round [334] log likelihood: -7853.281568
EM: Round [335] log likelihood: -7853.278353
EM: Round [336] log likelihood: -7853.275158
EM: Round [337] log likelihood: -7853.271983
EM: Round [338] log likelihood: -7853.268826
EM: Round [339] log likelihood: -7853.265689
EM: Round [340] log likelihood: -7853.262570
EM: Round [341] log likelihood: -7853.259470
EM: Round [342] log likelihood: -7853.256388
EM: Round [343] log likelihood: -7853.253325
EM: Round [344] log likelihood: -7853.250280
EM: Round [345] log likelihood: -7853.247253
EM: Round [346] log likelihood: -7853.244244
EM: Round [347] log likelihood: -7853.241254
EM: Round [348] log likelihood: -7853.238281
EM: Round [349] log likelihood: -7853.235326
EM: Round [350] log likelihood: -7853.232388
EM: Round [351] log likelihood: -7853.229468
EM: Round [352] log likelihood: -7853.226565
EM: Round [353] log likelihood: -7853.223679
EM: Round [354] log likelihood: -7853.220811
EM: Round [355] log likelihood: -7853.217959
EM: Round [356] log likelihood: -7853.215124
EM: Round [357] log likelihood: -7853.212307
EM: Round [358] log likelihood: -7853.209505
EM: Round [359] log likelihood: -7853.206721
EM: Round [360] log likelihood: -7853.203952
EM: Round [361] log likelihood: -7853.201200
EM: Round [362] log likelihood: -7853.198465
EM: Round [363] log likelihood: -7853.195745
EM: Round [364] log likelihood: -7853.193041
EM: Round [365] log likelihood: -7853.190354
EM: Round [366] log likelihood: -7853.187682
EM: Round [367] log likelihood: -7853.185025
EM: Round [368] log likelihood: -7853.182385
EM: Round [369] log likelihood: -7853.179760
EM: Round [370] log likelihood: -7853.177150
EM: Round [371] log likelihood: -7853.174555
EM: Round [372] log likelihood: -7853.171976
EM: Round [373] log likelihood: -7853.169412
EM: Round [374] log likelihood: -7853.166862
EM: Round [375] log likelihood: -7853.164328
EM: Round [376] log likelihood: -7853.161808
EM: Round [377] log likelihood: -7853.159304
EM: Round [378] log likelihood: -7853.156813
EM: Round [379] log likelihood: -7853.154337
EM: Round [380] log likelihood: -7853.151876
EM: Round [381] log likelihood: -7853.149429
EM: Round [382] log likelihood: -7853.146996
EM: Round [383] log likelihood: -7853.144577
EM: Round [384] log likelihood: -7853.142173
EM: Round [385] log likelihood: -7853.139782
EM: Round [386] log likelihood: -7853.137405
EM: Round [387] log likelihood: -7853.135042
EM: Round [388] log likelihood: -7853.132693
EM: Round [389] log likelihood: -7853.130357
EM: Round [390] log likelihood: -7853.128035
EM: Round [391] log likelihood: -7853.125726
EM: Round [392] log likelihood: -7853.123430
EM: Round [393] log likelihood: -7853.121148
EM: Round [394] log likelihood: -7853.118879
EM: Round [395] log likelihood: -7853.116623
EM: Round [396] log likelihood: -7853.114380
EM: Round [397] log likelihood: -7853.112149
EM: Round [398] log likelihood: -7853.109932
EM: Round [399] log likelihood: -7853.107728
EM: Round [400] log likelihood: -7853.105536
EM: Round [401] log likelihood: -7853.103356
EM: Round [402] log likelihood: -7853.101190
EM: Round [403] log likelihood: -7853.099035
EM: Round [404] log likelihood: -7853.096893
EM: Round [405] log likelihood: -7853.094764
EM: Round [406] log likelihood: -7853.092646
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EM: Round [862] log likelihood: -7852.740583
EM: Round [863] log likelihood: -7852.740403
EM: Round [864] log likelihood: -7852.740223
EM: Round [865] log likelihood: -7852.740045
EM: Round [866] log likelihood: -7852.739867
EM: Round [867] log likelihood: -7852.739690
EM: Round [868] log likelihood: -7852.739515
EM: Round [869] log likelihood: -7852.739340
EM: Round [870] log likelihood: -7852.739166
EM: Round [871] log likelihood: -7852.738993
EM: Round [872] log likelihood: -7852.738821
EM: Round [873] log likelihood: -7852.738649
EM: Round [874] log likelihood: -7852.738479
EM: Round [875] log likelihood: -7852.738310
EM: Round [876] log likelihood: -7852.738141
EM: Round [877] log likelihood: -7852.737974
EM: Round [878] log likelihood: -7852.737807
EM: Round [879] log likelihood: -7852.737641
EM: Round [880] log likelihood: -7852.737476
EM: Round [881] log likelihood: -7852.737312
EM: Round [882] log likelihood: -7852.737148
EM: Round [883] log likelihood: -7852.736986
EM: Round [884] log likelihood: -7852.736824
EM: Round [885] log likelihood: -7852.736663
EM: Round [886] log likelihood: -7852.736503
EM: Round [887] log likelihood: -7852.736344
EM: Round [888] log likelihood: -7852.736186
EM: Round [889] log likelihood: -7852.736028
EM: Round [890] log likelihood: -7852.735872
EM: Round [891] log likelihood: -7852.735716
EM: Round [892] log likelihood: -7852.735561
EM: Round [893] log likelihood: -7852.735407
EM: Round [894] log likelihood: -7852.735253
EM: Round [895] log likelihood: -7852.735101
EM: Round [896] log likelihood: -7852.734949
EM: Round [897] log likelihood: -7852.734798
EM: Round [898] log likelihood: -7852.734648
EM: Round [899] log likelihood: -7852.734498
EM: Round [900] log likelihood: -7852.734349
EM: Round [901] log likelihood: -7852.734202
EM: Round [902] log likelihood: -7852.734054
EM: Round [903] log likelihood: -7852.733908
EM: Round [904] log likelihood: -7852.733762
EM: Round [905] log likelihood: -7852.733618
EM: Round [906] log likelihood: -7852.733473
EM: Round [907] log likelihood: -7852.733330
EM: Round [908] log likelihood: -7852.733188
EM: Round [909] log likelihood: -7852.733046
EM: Round [910] log likelihood: -7852.732905
EM: Round [911] log likelihood: -7852.732764
EM: Round [912] log likelihood: -7852.732625
EM: Round [913] log likelihood: -7852.732486
EM: Round [914] log likelihood: -7852.732347
EM: Round [915] log likelihood: -7852.732210
EM: Round [916] log likelihood: -7852.732073
EM: Round [917] log likelihood: -7852.731937
EM: Round [918] log likelihood: -7852.731802
EM: Round [919] log likelihood: -7852.731667
EM: Round [920] log likelihood: -7852.731533
EM: Round [921] log likelihood: -7852.731400
EM: Round [922] log likelihood: -7852.731267
EM: Round [923] log likelihood: -7852.731136
EM: Round [924] log likelihood: -7852.731004
EM: Round [925] log likelihood: -7852.730874
EM: Round [926] log likelihood: -7852.730744
EM: Round [927] log likelihood: -7852.730615
EM: Round [928] log likelihood: -7852.730487
EM: Round [929] log likelihood: -7852.730359
EM: Round [930] log likelihood: -7852.730232
EM: Round [931] log likelihood: -7852.730105
EM: Round [932] log likelihood: -7852.729979
EM: Round [933] log likelihood: -7852.729854
EM: Round [934] log likelihood: -7852.729730
EM: Round [935] log likelihood: -7852.729606
EM: Round [936] log likelihood: -7852.729483
EM: Round [937] log likelihood: -7852.729360
EM: Round [938] log likelihood: -7852.729238
EM: Round [939] log likelihood: -7852.729117
EM: Round [940] log likelihood: -7852.728996
EM: Round [941] log likelihood: -7852.728876
EM: Round [942] log likelihood: -7852.728757
EM: Round [943] log likelihood: -7852.728638
EM: Round [944] log likelihood: -7852.728520
EM: Round [945] log likelihood: -7852.728402
EM: Round [946] log likelihood: -7852.728285
EM: Round [947] log likelihood: -7852.728169
EM: Round [948] log likelihood: -7852.728053
EM: Round [949] log likelihood: -7852.727938
EM: Round [950] log likelihood: -7852.727824
EM: Round [951] log likelihood: -7852.727710
EM: Round [952] log likelihood: -7852.727596
EM: Round [953] log likelihood: -7852.727484
EM: Round [954] log likelihood: -7852.727371
EM: Round [955] log likelihood: -7852.727260
EM: Round [956] log likelihood: -7852.727149
EM: Round [957] log likelihood: -7852.727038
EM: Round [958] log likelihood: -7852.726929
EM: Round [959] log likelihood: -7852.726819
EM: Round [960] log likelihood: -7852.726711
EM: Round [961] log likelihood: -7852.726602
EM: Round [962] log likelihood: -7852.726495
EM: Round [963] log likelihood: -7852.726388
EM: Round [964] log likelihood: -7852.726281
EM: Round [965] log likelihood: -7852.726175
EM: Round [966] log likelihood: -7852.726070
EM: Round [967] log likelihood: -7852.725965
EM: Round [968] log likelihood: -7852.725861
EM: Round [969] log likelihood: -7852.725757
EM: Round [970] log likelihood: -7852.725654
EM: Round [971] log likelihood: -7852.725551
EM: Round [972] log likelihood: -7852.725449
EM: Round [973] log likelihood: -7852.725348
EM: Round [974] log likelihood: -7852.725247
EM: Round [975] log likelihood: -7852.725146
EM: Round [976] log likelihood: -7852.725046
EM: Round [977] log likelihood: -7852.724947
EM: Stopping iterations at round 977 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir
-done, see /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -7097.961224
EM: Round [1] log likelihood: -7097.914278
EM: Round [2] log likelihood: -7097.914258
EM: Stopping iterations at round 2 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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 295604458
Execution Time = 5.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/fi_workdir/microH.dat
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.fqPNrqQpK0/fi_workdir/microH.dat /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/microH.dat /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fqPNrqQpK0 --json_outfile /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fqPNrqQpK0 --json_outfile /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory