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/8c/e6c241ebc43b61fc4c3f5e84912a16/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/e6c241ebc43b61fc4c3f5e84912a16/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/b118892a939ef3f5b1188399031feb/aih-tih-sc-284856-R1_A23WJ53LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/caf9b1e704a41117d1d180ee202eb0/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/b118892a939ef3f5b1188399031feb/aih-tih-sc-284856-R1_A23WJ53LT4_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 aih-tih-sc-284856-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-284856-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/cytoBand.txt
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.XJibhaNoI4/fi_workdir --reads "/tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 08:22:59 ..... started STAR run
Jun 08 08:22:59 ..... loading genome
Jun 08 08:24:47 ... generating Suffix Array index
Jun 08 08:28:58 ... completed Suffix Array index
Jun 08 08:28:59 ..... processing annotations GTF
Jun 08 08:28:59 ..... inserting junctions into the genome indices
Jun 08 08:30:09 ..... started mapping
Jun 08 08:46:43 ..... finished mapping
Jun 08 08:46:44 ..... started sorting BAM
Jun 08 08:46:45 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-284856-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-284856-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 23.79 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.XJibhaNoI4/fi_workdir --reads "/tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
08:46:55 : INFO : Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1520000] -done parsing /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 26,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 114,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 152,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 39,
'excessive soft clipping' => 10756,
'num genes matched < 2' => 16,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 40,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 156,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 564,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1402,
'seq-similar region overlap' => 81,
' ** passed ** ' => 5979,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
'per_id < 96' => 6745,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 264,
'small anchor length' => 32,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2250,
'exons hit < 2' => 34,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 258,
'low complexity anchor region' => 8
};
-writing fusion junction support info.
Execution Time = 0.99 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[642000] -fusion SPANNING read extraction for scaff: EEF1G--AHNAK
[1000]
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[31000] -fusion SPANNING read extraction for scaff: EFCAB14--CYP4A11
[1000]
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[43000] -fusion SPANNING read extraction for scaff: EIF4B--KRT3
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[41000] -fusion SPANNING read extraction for scaff: ERBIN--SREK1
[1000]
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[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: FAM222B--RBL1
[1000]
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[19000] -fusion SPANNING read extraction for scaff: FXR1--SOX2-OT
[1000]
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[8000]
[9000]
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[11000]
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[17000] -fusion SPANNING read extraction for scaff: GFPT1--RAB10
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[66000] -fusion SPANNING read extraction for scaff: HECTD4--VCL
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[66000] -fusion SPANNING read extraction for scaff: HECTD4--CASC11
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[14000] -fusion SPANNING read extraction for scaff: LINC00921--ELOB
[1000]
[2000] -fusion SPANNING read extraction for scaff: LRRC28--VSTM2B
[1000]
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[92000] -fusion SPANNING read extraction for scaff: MAP4--FBXW12
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[42000] -fusion SPANNING read extraction for scaff: NTRK3--NEPRO
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[47000] -fusion SPANNING read extraction for scaff: NTRK3--ABI3BP
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[20000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[18000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[21000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[9000] -fusion SPANNING read extraction for scaff: PLA2G6--FAM227A
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[8000]
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[17000] -fusion SPANNING read extraction for scaff: RAB10--GFPT1
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[82000] -fusion SPANNING read extraction for scaff: SETD2--SMARCC1
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[10000] -fusion SPANNING read extraction for scaff: STK4--KCNK15-AS1
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[8000]
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[10000] -fusion SPANNING read extraction for scaff: TRIM59--IFT80
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[5000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[11000] -fusion SPANNING read extraction for scaff: ZNF251--PIGF
[1000]
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[4000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
[1000]
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[7000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
[1000]
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[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000] -fusion SPANNING read extraction for scaff: ZNF7--EPAS1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 10983,
'lacks exon overlap' => 28053
};
Execution Time = 2.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7029.019043
EM: Round [1] log likelihood: -7026.826809
EM: Round [2] log likelihood: -7026.824489
EM: Round [3] log likelihood: -7026.822781
EM: Round [4] log likelihood: -7026.821082
EM: Round [5] log likelihood: -7026.819392
EM: Round [6] log likelihood: -7026.817710
EM: Round [7] log likelihood: -7026.816038
EM: Round [8] log likelihood: -7026.814373
EM: Round [9] log likelihood: -7026.812717
EM: Round [10] log likelihood: -7026.811070
EM: Round [11] log likelihood: -7026.809431
EM: Round [12] log likelihood: -7026.807801
EM: Round [13] log likelihood: -7026.806179
EM: Round [14] log likelihood: -7026.804565
EM: Round [15] log likelihood: -7026.802959
EM: Round [16] log likelihood: -7026.801361
EM: Round [17] log likelihood: -7026.799772
EM: Round [18] log likelihood: -7026.798190
EM: Round [19] log likelihood: -7026.796616
EM: Round [20] log likelihood: -7026.795051
EM: Round [21] log likelihood: -7026.793493
EM: Round [22] log likelihood: -7026.791943
EM: Round [23] log likelihood: -7026.790401
EM: Round [24] log likelihood: -7026.788866
EM: Round [25] log likelihood: -7026.787340
EM: Round [26] log likelihood: -7026.785820
EM: Round [27] log likelihood: -7026.784309
EM: Round [28] log likelihood: -7026.782805
EM: Round [29] log likelihood: -7026.781308
EM: Round [30] log likelihood: -7026.779819
EM: Round [31] log likelihood: -7026.778337
EM: Round [32] log likelihood: -7026.776863
EM: Round [33] log likelihood: -7026.775395
EM: Round [34] log likelihood: -7026.773935
EM: Round [35] log likelihood: -7026.772483
EM: Round [36] log likelihood: -7026.771037
EM: Round [37] log likelihood: -7026.769598
EM: Round [38] log likelihood: -7026.768167
EM: Round [39] log likelihood: -7026.766742
EM: Round [40] log likelihood: -7026.765325
EM: Round [41] log likelihood: -7026.763914
EM: Round [42] log likelihood: -7026.762511
EM: Round [43] log likelihood: -7026.761114
EM: Round [44] log likelihood: -7026.759723
EM: Round [45] log likelihood: -7026.758340
EM: Round [46] log likelihood: -7026.756963
EM: Round [47] log likelihood: -7026.755593
EM: Round [48] log likelihood: -7026.754230
EM: Round [49] log likelihood: -7026.752873
EM: Round [50] log likelihood: -7026.751523
EM: Round [51] log likelihood: -7026.750179
EM: Round [52] log likelihood: -7026.748842
EM: Round [53] log likelihood: -7026.747511
EM: Round [54] log likelihood: -7026.746187
EM: Round [55] log likelihood: -7026.744868
EM: Round [56] log likelihood: -7026.743556
EM: Round [57] log likelihood: -7026.742251
EM: Round [58] log likelihood: -7026.740952
EM: Round [59] log likelihood: -7026.739658
EM: Round [60] log likelihood: -7026.738371
EM: Round [61] log likelihood: -7026.737090
EM: Round [62] log likelihood: -7026.735816
EM: Round [63] log likelihood: -7026.734547
EM: Round [64] log likelihood: -7026.733284
EM: Round [65] log likelihood: -7026.732027
EM: Round [66] log likelihood: -7026.730776
EM: Round [67] log likelihood: -7026.729531
EM: Round [68] log likelihood: -7026.728292
EM: Round [69] log likelihood: -7026.727059
EM: Round [70] log likelihood: -7026.725831
EM: Round [71] log likelihood: -7026.724610
EM: Round [72] log likelihood: -7026.723394
EM: Round [73] log likelihood: -7026.722183
EM: Round [74] log likelihood: -7026.720979
EM: Round [75] log likelihood: -7026.719780
EM: Round [76] log likelihood: -7026.718586
EM: Round [77] log likelihood: -7026.717398
EM: Round [78] log likelihood: -7026.716216
EM: Round [79] log likelihood: -7026.715039
EM: Round [80] log likelihood: -7026.713868
EM: Round [81] log likelihood: -7026.712702
EM: Round [82] log likelihood: -7026.711541
EM: Round [83] log likelihood: -7026.710386
EM: Round [84] log likelihood: -7026.709236
EM: Round [85] log likelihood: -7026.708091
EM: Round [86] log likelihood: -7026.706952
EM: Round [87] log likelihood: -7026.705818
EM: Round [88] log likelihood: -7026.704689
EM: Round [89] log likelihood: -7026.703566
EM: Round [90] log likelihood: -7026.702447
EM: Round [91] log likelihood: -7026.701334
EM: Round [92] log likelihood: -7026.700226
EM: Round [93] log likelihood: -7026.699122
EM: Round [94] log likelihood: -7026.698024
EM: Round [95] log likelihood: -7026.696931
EM: Round [96] log likelihood: -7026.695843
EM: Round [97] log likelihood: -7026.694760
EM: Round [98] log likelihood: -7026.693682
EM: Round [99] log likelihood: -7026.692608
EM: Round [100] log likelihood: -7026.691540
EM: Round [101] log likelihood: -7026.690476
EM: Round [102] log likelihood: -7026.689417
EM: Round [103] log likelihood: -7026.688363
EM: Round [104] log likelihood: -7026.687314
EM: Round [105] log likelihood: -7026.686269
EM: Round [106] log likelihood: -7026.685230
EM: Round [107] log likelihood: -7026.684194
EM: Round [108] log likelihood: -7026.683164
EM: Round [109] log likelihood: -7026.682138
EM: Round [110] log likelihood: -7026.681117
EM: Round [111] log likelihood: -7026.680100
EM: Round [112] log likelihood: -7026.679088
EM: Round [113] log likelihood: -7026.678080
EM: Round [114] log likelihood: -7026.677077
EM: Round [115] log likelihood: -7026.676079
EM: Round [116] log likelihood: -7026.675085
EM: Round [117] log likelihood: -7026.674095
EM: Round [118] log likelihood: -7026.673110
EM: Round [119] log likelihood: -7026.672129
EM: Round [120] log likelihood: -7026.671152
EM: Round [121] log likelihood: -7026.670180
EM: Round [122] log likelihood: -7026.669212
EM: Round [123] log likelihood: -7026.668249
EM: Round [124] log likelihood: -7026.667289
EM: Round [125] log likelihood: -7026.666334
EM: Round [126] log likelihood: -7026.665383
EM: Round [127] log likelihood: -7026.664437
EM: Round [128] log likelihood: -7026.663494
EM: Round [129] log likelihood: -7026.662556
EM: Round [130] log likelihood: -7026.661622
EM: Round [131] log likelihood: -7026.660692
EM: Round [132] log likelihood: -7026.659766
EM: Round [133] log likelihood: -7026.658844
EM: Round [134] log likelihood: -7026.657926
EM: Round [135] log likelihood: -7026.657012
EM: Round [136] log likelihood: -7026.656102
EM: Round [137] log likelihood: -7026.655197
EM: Round [138] log likelihood: -7026.654295
EM: Round [139] log likelihood: -7026.653397
EM: Round [140] log likelihood: -7026.652503
EM: Round [141] log likelihood: -7026.651613
EM: Round [142] log likelihood: -7026.650726
EM: Round [143] log likelihood: -7026.649844
EM: Round [144] log likelihood: -7026.648965
EM: Round [145] log likelihood: -7026.648091
EM: Round [146] log likelihood: -7026.647220
EM: Round [147] log likelihood: -7026.646352
EM: Round [148] log likelihood: -7026.645489
EM: Round [149] log likelihood: -7026.644629
EM: Round [150] log likelihood: -7026.643773
EM: Round [151] log likelihood: -7026.642921
EM: Round [152] log likelihood: -7026.642073
EM: Round [153] log likelihood: -7026.641228
EM: Round [154] log likelihood: -7026.640386
EM: Round [155] log likelihood: -7026.639549
EM: Round [156] log likelihood: -7026.638715
EM: Round [157] log likelihood: -7026.637884
EM: Round [158] log likelihood: -7026.637057
EM: Round [159] log likelihood: -7026.636234
EM: Round [160] log likelihood: -7026.635414
EM: Round [161] log likelihood: -7026.634598
EM: Round [162] log likelihood: -7026.633785
EM: Round [163] log likelihood: -7026.632976
EM: Round [164] log likelihood: -7026.632170
EM: Round [165] log likelihood: -7026.631368
EM: Round [166] log likelihood: -7026.630569
EM: Round [167] log likelihood: -7026.629773
EM: Round [168] log likelihood: -7026.628981
EM: Round [169] log likelihood: -7026.628192
EM: Round [170] log likelihood: -7026.627407
EM: Round [171] log likelihood: -7026.626625
EM: Round [172] log likelihood: -7026.625846
EM: Round [173] log likelihood: -7026.625071
EM: Round [174] log likelihood: -7026.624298
EM: Round [175] log likelihood: -7026.623529
EM: Round [176] log likelihood: -7026.622764
EM: Round [177] log likelihood: -7026.622001
EM: Round [178] log likelihood: -7026.621242
EM: Round [179] log likelihood: -7026.620486
EM: Round [180] log likelihood: -7026.619734
EM: Round [181] log likelihood: -7026.618984
EM: Round [182] log likelihood: -7026.618237
EM: Round [183] log likelihood: -7026.617494
EM: Round [184] log likelihood: -7026.616754
EM: Round [185] log likelihood: -7026.616017
EM: Round [186] log likelihood: -7026.615283
EM: Round [187] log likelihood: -7026.614552
EM: Round [188] log likelihood: -7026.613824
EM: Round [189] log likelihood: -7026.613100
EM: Round [190] log likelihood: -7026.612378
EM: Round [191] log likelihood: -7026.611659
EM: Round [192] log likelihood: -7026.610944
EM: Round [193] log likelihood: -7026.610231
EM: Round [194] log likelihood: -7026.609521
EM: Round [195] log likelihood: -7026.608815
EM: Round [196] log likelihood: -7026.608111
EM: Round [197] log likelihood: -7026.607410
EM: Round [198] log likelihood: -7026.606712
EM: Round [199] log likelihood: -7026.606017
EM: Round [200] log likelihood: -7026.605325
EM: Round [201] log likelihood: -7026.604636
EM: Round [202] log likelihood: -7026.603949
EM: Round [203] log likelihood: -7026.603266
EM: Round [204] log likelihood: -7026.602585
EM: Round [205] log likelihood: -7026.601907
EM: Round [206] log likelihood: -7026.601232
EM: Round [207] log likelihood: -7026.600560
EM: Round [208] log likelihood: -7026.599890
EM: Round [209] log likelihood: -7026.599224
EM: Round [210] log likelihood: -7026.598560
EM: Round [211] log likelihood: -7026.597899
EM: Round [212] log likelihood: -7026.597240
EM: Round [213] log likelihood: -7026.596584
EM: Round [214] log likelihood: -7026.595931
EM: Round [215] log likelihood: -7026.595281
EM: Round [216] log likelihood: -7026.594633
EM: Round [217] log likelihood: -7026.593988
EM: Round [218] log likelihood: -7026.593346
EM: Round [219] log likelihood: -7026.592706
EM: Round [220] log likelihood: -7026.592069
EM: Round [221] log likelihood: -7026.591435
EM: Round [222] log likelihood: -7026.590803
EM: Round [223] log likelihood: -7026.590174
EM: Round [224] log likelihood: -7026.589547
EM: Round [225] log likelihood: -7026.588923
EM: Round [226] log likelihood: -7026.588301
EM: Round [227] log likelihood: -7026.587682
EM: Round [228] log likelihood: -7026.587066
EM: Round [229] log likelihood: -7026.586452
EM: Round [230] log likelihood: -7026.585840
EM: Round [231] log likelihood: -7026.585231
EM: Round [232] log likelihood: -7026.584625
EM: Round [233] log likelihood: -7026.584021
EM: Round [234] log likelihood: -7026.583419
EM: Round [235] log likelihood: -7026.582820
EM: Round [236] log likelihood: -7026.582223
EM: Round [237] log likelihood: -7026.581629
EM: Round [238] log likelihood: -7026.581037
EM: Round [239] log likelihood: -7026.580448
EM: Round [240] log likelihood: -7026.579861
EM: Round [241] log likelihood: -7026.579276
EM: Round [242] log likelihood: -7026.578694
EM: Round [243] log likelihood: -7026.578114
EM: Round [244] log likelihood: -7026.577536
EM: Round [245] log likelihood: -7026.576961
EM: Round [246] log likelihood: -7026.576388
EM: Round [247] log likelihood: -7026.575818
EM: Round [248] log likelihood: -7026.575249
EM: Round [249] log likelihood: -7026.574683
EM: Round [250] log likelihood: -7026.574120
EM: Round [251] log likelihood: -7026.573558
EM: Round [252] log likelihood: -7026.572999
EM: Round [253] log likelihood: -7026.572442
EM: Round [254] log likelihood: -7026.571887
EM: Round [255] log likelihood: -7026.571335
EM: Round [256] log likelihood: -7026.570785
EM: Round [257] log likelihood: -7026.570237
EM: Round [258] log likelihood: -7026.569691
EM: Round [259] log likelihood: -7026.569147
EM: Round [260] log likelihood: -7026.568606
EM: Round [261] log likelihood: -7026.568066
EM: Round [262] log likelihood: -7026.567529
EM: Round [263] log likelihood: -7026.566994
EM: Round [264] log likelihood: -7026.566462
EM: Round [265] log likelihood: -7026.565931
EM: Round [266] log likelihood: -7026.565402
EM: Round [267] log likelihood: -7026.564876
EM: Round [268] log likelihood: -7026.564352
EM: Round [269] log likelihood: -7026.563829
EM: Round [270] log likelihood: -7026.563309
EM: Round [271] log likelihood: -7026.562791
EM: Round [272] log likelihood: -7026.562275
EM: Round [273] log likelihood: -7026.561761
EM: Round [274] log likelihood: -7026.561249
EM: Round [275] log likelihood: -7026.560739
EM: Round [276] log likelihood: -7026.560231
EM: Round [277] log likelihood: -7026.559725
EM: Round [278] log likelihood: -7026.559222
EM: Round [279] log likelihood: -7026.558720
EM: Round [280] log likelihood: -7026.558220
EM: Round [281] log likelihood: -7026.557722
EM: Round [282] log likelihood: -7026.557226
EM: Round [283] log likelihood: -7026.556732
EM: Round [284] log likelihood: -7026.556240
EM: Round [285] log likelihood: -7026.555750
EM: Round [286] log likelihood: -7026.555262
EM: Round [287] log likelihood: -7026.554776
EM: Round [288] log likelihood: -7026.554292
EM: Round [289] log likelihood: -7026.553810
EM: Round [290] log likelihood: -7026.553329
EM: Round [291] log likelihood: -7026.552851
EM: Round [292] log likelihood: -7026.552374
EM: Round [293] log likelihood: -7026.551900
EM: Round [294] log likelihood: -7026.551427
EM: Round [295] log likelihood: -7026.550956
EM: Round [296] log likelihood: -7026.550487
EM: Round [297] log likelihood: -7026.550019
EM: Round [298] log likelihood: -7026.549554
EM: Round [299] log likelihood: -7026.549090
EM: Round [300] log likelihood: -7026.548629
EM: Round [301] log likelihood: -7026.548169
EM: Round [302] log likelihood: -7026.547710
EM: Round [303] log likelihood: -7026.547254
EM: Round [304] log likelihood: -7026.546799
EM: Round [305] log likelihood: -7026.546347
EM: Round [306] log likelihood: -7026.545896
EM: Round [307] log likelihood: -7026.545446
EM: Round [308] log likelihood: -7026.544999
EM: Round [309] log likelihood: -7026.544553
EM: Round [310] log likelihood: -7026.544109
EM: Round [311] log likelihood: -7026.543667
EM: Round [312] log likelihood: -7026.543227
EM: Round [313] log likelihood: -7026.542788
EM: Round [314] log likelihood: -7026.542351
EM: Round [315] log likelihood: -7026.541915
EM: Round [316] log likelihood: -7026.541482
EM: Round [317] log likelihood: -7026.541050
EM: Round [318] log likelihood: -7026.540619
EM: Round [319] log likelihood: -7026.540191
EM: Round [320] log likelihood: -7026.539764
EM: Round [321] log likelihood: -7026.539339
EM: Round [322] log likelihood: -7026.538915
EM: Round [323] log likelihood: -7026.538493
EM: Round [324] log likelihood: -7026.538073
EM: Round [325] log likelihood: -7026.537654
EM: Round [326] log likelihood: -7026.537237
EM: Round [327] log likelihood: -7026.536821
EM: Round [328] log likelihood: -7026.536408
EM: Round [329] log likelihood: -7026.535995
EM: Round [330] log likelihood: -7026.535585
EM: Round [331] log likelihood: -7026.535176
EM: Round [332] log likelihood: -7026.534768
EM: Round [333] log likelihood: -7026.534362
EM: Round [334] log likelihood: -7026.533958
EM: Round [335] log likelihood: -7026.533555
EM: Round [336] log likelihood: -7026.533154
EM: Round [337] log likelihood: -7026.532755
EM: Round [338] log likelihood: -7026.532357
EM: Round [339] log likelihood: -7026.531960
EM: Round [340] log likelihood: -7026.531565
EM: Round [341] log likelihood: -7026.531172
EM: Round [342] log likelihood: -7026.530780
EM: Round [343] log likelihood: -7026.530389
EM: Round [344] log likelihood: -7026.530000
EM: Round [345] log likelihood: -7026.529613
EM: Round [346] log likelihood: -7026.529227
EM: Round [347] log likelihood: -7026.528843
EM: Round [348] log likelihood: -7026.528460
EM: Round [349] log likelihood: -7026.528078
EM: Round [350] log likelihood: -7026.527698
EM: Round [351] log likelihood: -7026.527320
EM: Round [352] log likelihood: -7026.526943
EM: Round [353] log likelihood: -7026.526567
EM: Round [354] log likelihood: -7026.526193
EM: Round [355] log likelihood: -7026.525820
EM: Round [356] log likelihood: -7026.525449
EM: Round [357] log likelihood: -7026.525079
EM: Round [358] log likelihood: -7026.524710
EM: Round [359] log likelihood: -7026.524343
EM: Round [360] log likelihood: -7026.523978
EM: Round [361] log likelihood: -7026.523613
EM: Round [362] log likelihood: -7026.523250
EM: Round [363] log likelihood: -7026.522889
EM: Round [364] log likelihood: -7026.522529
EM: Round [365] log likelihood: -7026.522170
EM: Round [366] log likelihood: -7026.521813
EM: Round [367] log likelihood: -7026.521457
EM: Round [368] log likelihood: -7026.521102
EM: Round [369] log likelihood: -7026.520749
EM: Round [370] log likelihood: -7026.520397
EM: Round [371] log likelihood: -7026.520047
EM: Round [372] log likelihood: -7026.519697
EM: Round [373] log likelihood: -7026.519350
EM: Round [374] log likelihood: -7026.519003
EM: Round [375] log likelihood: -7026.518658
EM: Round [376] log likelihood: -7026.518314
EM: Round [377] log likelihood: -7026.517971
EM: Round [378] log likelihood: -7026.517630
EM: Round [379] log likelihood: -7026.517290
EM: Round [380] log likelihood: -7026.516951
EM: Round [381] log likelihood: -7026.516614
EM: Round [382] log likelihood: -7026.516278
EM: Round [383] log likelihood: -7026.515943
EM: Round [384] log likelihood: -7026.515610
EM: Round [385] log likelihood: -7026.515277
EM: Round [386] log likelihood: -7026.514946
EM: Round [387] log likelihood: -7026.514616
EM: Round [388] log likelihood: -7026.514288
EM: Round [389] log likelihood: -7026.513961
EM: Round [390] log likelihood: -7026.513635
EM: Round [391] log likelihood: -7026.513310
EM: Round [392] log likelihood: -7026.512986
EM: Round [393] log likelihood: -7026.512664
EM: Round [394] log likelihood: -7026.512343
EM: Round [395] log likelihood: -7026.512023
EM: Round [396] log likelihood: -7026.511704
EM: Round [397] log likelihood: -7026.511387
EM: Round [398] log likelihood: -7026.511071
EM: Round [399] log likelihood: -7026.510756
EM: Round [400] log likelihood: -7026.510442
EM: Round [401] log likelihood: -7026.510129
EM: Round [402] log likelihood: -7026.509818
EM: Round [403] log likelihood: -7026.509507
EM: Round [404] log likelihood: -7026.509198
EM: Round [405] log likelihood: -7026.508890
EM: Round [406] log likelihood: -7026.508583
EM: Round [407] log likelihood: -7026.508278
EM: Round [408] log likelihood: -7026.507973
EM: Round [409] log likelihood: -7026.507670
EM: Round [410] log likelihood: -7026.507368
EM: Round [411] log likelihood: -7026.507066
EM: Round [412] log likelihood: -7026.506767
EM: Round [413] log likelihood: -7026.506468
EM: Round [414] log likelihood: -7026.506170
EM: Round [415] log likelihood: -7026.505874
EM: Round [416] log likelihood: -7026.505578
EM: Round [417] log likelihood: -7026.505284
EM: Round [418] log likelihood: -7026.504991
EM: Round [419] log likelihood: -7026.504698
EM: Round [420] log likelihood: -7026.504407
EM: Round [421] log likelihood: -7026.504118
EM: Round [422] log likelihood: -7026.503829
EM: Round [423] log likelihood: -7026.503541
EM: Round [424] log likelihood: -7026.503254
EM: Round [425] log likelihood: -7026.502969
EM: Round [426] log likelihood: -7026.502684
EM: Round [427] log likelihood: -7026.502401
EM: Round [428] log likelihood: -7026.502118
EM: Round [429] log likelihood: -7026.501837
EM: Round [430] log likelihood: -7026.501557
EM: Round [431] log likelihood: -7026.501278
EM: Round [432] log likelihood: -7026.500999
EM: Round [433] log likelihood: -7026.500722
EM: Round [434] log likelihood: -7026.500446
EM: Round [435] log likelihood: -7026.500171
EM: Round [436] log likelihood: -7026.499897
EM: Round [437] log likelihood: -7026.499624
EM: Round [438] log likelihood: -7026.499352
EM: Round [439] log likelihood: -7026.499081
EM: Round [440] log likelihood: -7026.498811
EM: Round [441] log likelihood: -7026.498542
EM: Round [442] log likelihood: -7026.498274
EM: Round [443] log likelihood: -7026.498008
EM: Round [444] log likelihood: -7026.497742
EM: Round [445] log likelihood: -7026.497477
EM: Round [446] log likelihood: -7026.497213
EM: Round [447] log likelihood: -7026.496950
EM: Round [448] log likelihood: -7026.496688
EM: Round [449] log likelihood: -7026.496427
EM: Round [450] log likelihood: -7026.496167
EM: Round [451] log likelihood: -7026.495908
EM: Round [452] log likelihood: -7026.495650
EM: Round [453] log likelihood: -7026.495393
EM: Round [454] log likelihood: -7026.495136
EM: Round [455] log likelihood: -7026.494881
EM: Round [456] log likelihood: -7026.494627
EM: Round [457] log likelihood: -7026.494374
EM: Round [458] log likelihood: -7026.494121
EM: Round [459] log likelihood: -7026.493870
EM: Round [460] log likelihood: -7026.493619
EM: Round [461] log likelihood: -7026.493370
EM: Round [462] log likelihood: -7026.493121
EM: Round [463] log likelihood: -7026.492874
EM: Round [464] log likelihood: -7026.492627
EM: Round [465] log likelihood: -7026.492381
EM: Round [466] log likelihood: -7026.492136
EM: Round [467] log likelihood: -7026.491892
EM: Round [468] log likelihood: -7026.491649
EM: Round [469] log likelihood: -7026.491407
EM: Round [470] log likelihood: -7026.491165
EM: Round [471] log likelihood: -7026.490925
EM: Round [472] log likelihood: -7026.490685
EM: Round [473] log likelihood: -7026.490447
EM: Round [474] log likelihood: -7026.490209
EM: Round [475] log likelihood: -7026.489972
EM: Round [476] log likelihood: -7026.489736
EM: Round [477] log likelihood: -7026.489501
EM: Round [478] log likelihood: -7026.489266
EM: Round [479] log likelihood: -7026.489033
EM: Round [480] log likelihood: -7026.488801
EM: Round [481] log likelihood: -7026.488569
EM: Round [482] log likelihood: -7026.488338
EM: Round [483] log likelihood: -7026.488108
EM: Round [484] log likelihood: -7026.487879
EM: Round [485] log likelihood: -7026.487651
EM: Round [486] log likelihood: -7026.487423
EM: Round [487] log likelihood: -7026.487197
EM: Round [488] log likelihood: -7026.486971
EM: Round [489] log likelihood: -7026.486746
EM: Round [490] log likelihood: -7026.486522
EM: Round [491] log likelihood: -7026.486299
EM: Round [492] log likelihood: -7026.486076
EM: Round [493] log likelihood: -7026.485855
EM: Round [494] log likelihood: -7026.485634
EM: Round [495] log likelihood: -7026.485414
EM: Round [496] log likelihood: -7026.485195
EM: Round [497] log likelihood: -7026.484977
EM: Round [498] log likelihood: -7026.484759
EM: Round [499] log likelihood: -7026.484542
EM: Round [500] log likelihood: -7026.484326
EM: Round [501] log likelihood: -7026.484111
EM: Round [502] log likelihood: -7026.483897
EM: Round [503] log likelihood: -7026.483683
EM: Round [504] log likelihood: -7026.483471
EM: Round [505] log likelihood: -7026.483259
EM: Round [506] log likelihood: -7026.483047
EM: Round [507] log likelihood: -7026.482837
EM: Round [508] log likelihood: -7026.482627
EM: Round [509] log likelihood: -7026.482419
EM: Round [510] log likelihood: -7026.482210
EM: Round [511] log likelihood: -7026.482003
EM: Round [512] log likelihood: -7026.481796
EM: Round [513] log likelihood: -7026.481591
EM: Round [514] log likelihood: -7026.481386
EM: Round [515] log likelihood: -7026.481181
EM: Round [516] log likelihood: -7026.480978
EM: Round [517] log likelihood: -7026.480775
EM: Round [518] log likelihood: -7026.480573
EM: Round [519] log likelihood: -7026.480372
EM: Round [520] log likelihood: -7026.480171
EM: Round [521] log likelihood: -7026.479971
EM: Round [522] log likelihood: -7026.479772
EM: Round [523] log likelihood: -7026.479574
EM: Round [524] log likelihood: -7026.479376
EM: Round [525] log likelihood: -7026.479179
EM: Round [526] log likelihood: -7026.478983
EM: Round [527] log likelihood: -7026.478787
EM: Round [528] log likelihood: -7026.478593
EM: Round [529] log likelihood: -7026.478399
EM: Round [530] log likelihood: -7026.478205
EM: Round [531] log likelihood: -7026.478013
EM: Round [532] log likelihood: -7026.477821
EM: Round [533] log likelihood: -7026.477629
EM: Round [534] log likelihood: -7026.477439
EM: Round [535] log likelihood: -7026.477249
EM: Round [536] log likelihood: -7026.477060
EM: Round [537] log likelihood: -7026.476871
EM: Round [538] log likelihood: -7026.476684
EM: Round [539] log likelihood: -7026.476497
EM: Round [540] log likelihood: -7026.476310
EM: Round [541] log likelihood: -7026.476125
EM: Round [542] log likelihood: -7026.475940
EM: Round [543] log likelihood: -7026.475755
EM: Round [544] log likelihood: -7026.475572
EM: Round [545] log likelihood: -7026.475389
EM: Round [546] log likelihood: -7026.475206
EM: Round [547] log likelihood: -7026.475025
EM: Round [548] log likelihood: -7026.474844
EM: Round [549] log likelihood: -7026.474663
EM: Round [550] log likelihood: -7026.474484
EM: Round [551] log likelihood: -7026.474304
EM: Round [552] log likelihood: -7026.474126
EM: Round [553] log likelihood: -7026.473948
EM: Round [554] log likelihood: -7026.473771
EM: Round [555] log likelihood: -7026.473595
EM: Round [556] log likelihood: -7026.473419
EM: Round [557] log likelihood: -7026.473244
EM: Round [558] log likelihood: -7026.473069
EM: Round [559] log likelihood: -7026.472896
EM: Round [560] log likelihood: -7026.472722
EM: Round [561] log likelihood: -7026.472550
EM: Round [562] log likelihood: -7026.472378
EM: Round [563] log likelihood: -7026.472206
EM: Round [564] log likelihood: -7026.472036
EM: Round [565] log likelihood: -7026.471866
EM: Round [566] log likelihood: -7026.471696
EM: Round [567] log likelihood: -7026.471527
EM: Round [568] log likelihood: -7026.471359
EM: Round [569] log likelihood: -7026.471191
EM: Round [570] log likelihood: -7026.471024
EM: Round [571] log likelihood: -7026.470858
EM: Round [572] log likelihood: -7026.470692
EM: Round [573] log likelihood: -7026.470527
EM: Round [574] log likelihood: -7026.470362
EM: Round [575] log likelihood: -7026.470198
EM: Round [576] log likelihood: -7026.470035
EM: Round [577] log likelihood: -7026.469872
EM: Round [578] log likelihood: -7026.469710
EM: Round [579] log likelihood: -7026.469548
EM: Round [580] log likelihood: -7026.469387
EM: Round [581] log likelihood: -7026.469227
EM: Round [582] log likelihood: -7026.469067
EM: Round [583] log likelihood: -7026.468908
EM: Round [584] log likelihood: -7026.468749
EM: Round [585] log likelihood: -7026.468591
EM: Round [586] log likelihood: -7026.468433
EM: Round [587] log likelihood: -7026.468276
EM: Round [588] log likelihood: -7026.468120
EM: Round [589] log likelihood: -7026.467964
EM: Round [590] log likelihood: -7026.467809
EM: Round [591] log likelihood: -7026.467654
EM: Round [592] log likelihood: -7026.467500
EM: Round [593] log likelihood: -7026.467346
EM: Round [594] log likelihood: -7026.467193
EM: Round [595] log likelihood: -7026.467040
EM: Round [596] log likelihood: -7026.466888
EM: Round [597] log likelihood: -7026.466737
EM: Round [598] log likelihood: -7026.466586
EM: Round [599] log likelihood: -7026.466436
EM: Round [600] log likelihood: -7026.466286
EM: Round [601] log likelihood: -7026.466137
EM: Round [602] log likelihood: -7026.465988
EM: Round [603] log likelihood: -7026.465840
EM: Round [604] log likelihood: -7026.465693
EM: Round [605] log likelihood: -7026.465545
EM: Round [606] log likelihood: -7026.465399
EM: Round [607] log likelihood: -7026.465253
EM: Round [608] log likelihood: -7026.465107
EM: Round [609] log likelihood: -7026.464962
EM: Round [610] log likelihood: -7026.464818
EM: Round [611] log likelihood: -7026.464674
EM: Round [612] log likelihood: -7026.464531
EM: Round [613] log likelihood: -7026.464388
EM: Round [614] log likelihood: -7026.464246
EM: Round [615] log likelihood: -7026.464104
EM: Round [616] log likelihood: -7026.463962
EM: Round [617] log likelihood: -7026.463822
EM: Round [618] log likelihood: -7026.463681
EM: Round [619] log likelihood: -7026.463541
EM: Round [620] log likelihood: -7026.463402
EM: Round [621] log likelihood: -7026.463263
EM: Round [622] log likelihood: -7026.463125
EM: Round [623] log likelihood: -7026.462987
EM: Round [624] log likelihood: -7026.462850
EM: Round [625] log likelihood: -7026.462713
EM: Round [626] log likelihood: -7026.462577
EM: Round [627] log likelihood: -7026.462441
EM: Round [628] log likelihood: -7026.462306
EM: Round [629] log likelihood: -7026.462171
EM: Round [630] log likelihood: -7026.462037
EM: Round [631] log likelihood: -7026.461903
EM: Round [632] log likelihood: -7026.461769
EM: Round [633] log likelihood: -7026.461636
EM: Round [634] log likelihood: -7026.461504
EM: Round [635] log likelihood: -7026.461372
EM: Round [636] log likelihood: -7026.461241
EM: Round [637] log likelihood: -7026.461110
EM: Round [638] log likelihood: -7026.460979
EM: Round [639] log likelihood: -7026.460849
EM: Round [640] log likelihood: -7026.460720
EM: Round [641] log likelihood: -7026.460590
EM: Round [642] log likelihood: -7026.460462
EM: Round [643] log likelihood: -7026.460334
EM: Round [644] log likelihood: -7026.460206
EM: Round [645] log likelihood: -7026.460079
EM: Round [646] log likelihood: -7026.459952
EM: Round [647] log likelihood: -7026.459825
EM: Round [648] log likelihood: -7026.459700
EM: Round [649] log likelihood: -7026.459574
EM: Round [650] log likelihood: -7026.459449
EM: Round [651] log likelihood: -7026.459325
EM: Round [652] log likelihood: -7026.459200
EM: Round [653] log likelihood: -7026.459077
EM: Round [654] log likelihood: -7026.458954
EM: Round [655] log likelihood: -7026.458831
EM: Round [656] log likelihood: -7026.458708
EM: Round [657] log likelihood: -7026.458587
EM: Round [658] log likelihood: -7026.458465
EM: Round [659] log likelihood: -7026.458344
EM: Round [660] log likelihood: -7026.458224
EM: Round [661] log likelihood: -7026.458103
EM: Round [662] log likelihood: -7026.457984
EM: Round [663] log likelihood: -7026.457864
EM: Round [664] log likelihood: -7026.457746
EM: Round [665] log likelihood: -7026.457627
EM: Round [666] log likelihood: -7026.457509
EM: Round [667] log likelihood: -7026.457392
EM: Round [668] log likelihood: -7026.457274
EM: Round [669] log likelihood: -7026.457158
EM: Round [670] log likelihood: -7026.457041
EM: Round [671] log likelihood: -7026.456926
EM: Round [672] log likelihood: -7026.456810
EM: Round [673] log likelihood: -7026.456695
EM: Round [674] log likelihood: -7026.456580
EM: Round [675] log likelihood: -7026.456466
EM: Round [676] log likelihood: -7026.456352
EM: Round [677] log likelihood: -7026.456239
EM: Round [678] log likelihood: -7026.456126
EM: Round [679] log likelihood: -7026.456013
EM: Round [680] log likelihood: -7026.455901
EM: Round [681] log likelihood: -7026.455789
EM: Round [682] log likelihood: -7026.455678
EM: Round [683] log likelihood: -7026.455567
EM: Round [684] log likelihood: -7026.455456
EM: Round [685] log likelihood: -7026.455346
EM: Round [686] log likelihood: -7026.455236
EM: Round [687] log likelihood: -7026.455127
EM: Round [688] log likelihood: -7026.455018
EM: Round [689] log likelihood: -7026.454909
EM: Round [690] log likelihood: -7026.454801
EM: Round [691] log likelihood: -7026.454693
EM: Round [692] log likelihood: -7026.454585
EM: Round [693] log likelihood: -7026.454478
EM: Round [694] log likelihood: -7026.454372
EM: Round [695] log likelihood: -7026.454265
EM: Round [696] log likelihood: -7026.454159
EM: Round [697] log likelihood: -7026.454054
EM: Round [698] log likelihood: -7026.453949
EM: Round [699] log likelihood: -7026.453844
EM: Round [700] log likelihood: -7026.453739
EM: Round [701] log likelihood: -7026.453635
EM: Round [702] log likelihood: -7026.453532
EM: Round [703] log likelihood: -7026.453428
EM: Round [704] log likelihood: -7026.453325
EM: Round [705] log likelihood: -7026.453223
EM: Round [706] log likelihood: -7026.453121
EM: Round [707] log likelihood: -7026.453019
EM: Round [708] log likelihood: -7026.452917
EM: Round [709] log likelihood: -7026.452816
EM: Round [710] log likelihood: -7026.452715
EM: Round [711] log likelihood: -7026.452615
EM: Round [712] log likelihood: -7026.452515
EM: Round [713] log likelihood: -7026.452415
EM: Stopping iterations at round 713 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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/aih-tih-sc-284856-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa > /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir
-done, see /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6679.692470
EM: Round [1] log likelihood: -6678.451606
EM: Round [2] log likelihood: -6678.447648
EM: Round [3] log likelihood: -6678.444253
EM: Round [4] log likelihood: -6678.440881
EM: Round [5] log likelihood: -6678.437532
EM: Round [6] log likelihood: -6678.434206
EM: Round [7] log likelihood: -6678.430902
EM: Round [8] log likelihood: -6678.427621
EM: Round [9] log likelihood: -6678.424361
EM: Round [10] log likelihood: -6678.421124
EM: Round [11] log likelihood: -6678.417908
EM: Round [12] log likelihood: -6678.414714
EM: Round [13] log likelihood: -6678.411541
EM: Round [14] log likelihood: -6678.408388
EM: Round [15] log likelihood: -6678.405257
EM: Round [16] log likelihood: -6678.402146
EM: Round [17] log likelihood: -6678.399056
EM: Round [18] log likelihood: -6678.395986
EM: Round [19] log likelihood: -6678.392936
EM: Round [20] log likelihood: -6678.389905
EM: Round [21] log likelihood: -6678.386895
EM: Round [22] log likelihood: -6678.383903
EM: Round [23] log likelihood: -6678.380931
EM: Round [24] log likelihood: -6678.377978
EM: Round [25] log likelihood: -6678.375044
EM: Round [26] log likelihood: -6678.372129
EM: Round [27] log likelihood: -6678.369232
EM: Round [28] log likelihood: -6678.366354
EM: Round [29] log likelihood: -6678.363494
EM: Round [30] log likelihood: -6678.360652
EM: Round [31] log likelihood: -6678.357827
EM: Round [32] log likelihood: -6678.355021
EM: Round [33] log likelihood: -6678.352232
EM: Round [34] log likelihood: -6678.349460
EM: Round [35] log likelihood: -6678.346706
EM: Round [36] log likelihood: -6678.343969
EM: Round [37] log likelihood: -6678.341249
EM: Round [38] log likelihood: -6678.338545
EM: Round [39] log likelihood: -6678.335858
EM: Round [40] log likelihood: -6678.333188
EM: Round [41] log likelihood: -6678.330534
EM: Round [42] log likelihood: -6678.327896
EM: Round [43] log likelihood: -6678.325274
EM: Round [44] log likelihood: -6678.322669
EM: Round [45] log likelihood: -6678.320079
EM: Round [46] log likelihood: -6678.317504
EM: Round [47] log likelihood: -6678.314945
EM: Round [48] log likelihood: -6678.312402
EM: Round [49] log likelihood: -6678.309874
EM: Round [50] log likelihood: -6678.307360
EM: Round [51] log likelihood: -6678.304862
EM: Round [52] log likelihood: -6678.302379
EM: Round [53] log likelihood: -6678.299911
EM: Round [54] log likelihood: -6678.297457
EM: Round [55] log likelihood: -6678.295017
EM: Round [56] log likelihood: -6678.292592
EM: Round [57] log likelihood: -6678.290182
EM: Round [58] log likelihood: -6678.287785
EM: Round [59] log likelihood: -6678.285402
EM: Round [60] log likelihood: -6678.283034
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EM: Round [521] log likelihood: -6677.849695
EM: Round [522] log likelihood: -6677.849387
EM: Round [523] log likelihood: -6677.849081
EM: Round [524] log likelihood: -6677.848776
EM: Round [525] log likelihood: -6677.848472
EM: Round [526] log likelihood: -6677.848169
EM: Round [527] log likelihood: -6677.847867
EM: Round [528] log likelihood: -6677.847567
EM: Round [529] log likelihood: -6677.847267
EM: Round [530] log likelihood: -6677.846969
EM: Round [531] log likelihood: -6677.846672
EM: Round [532] log likelihood: -6677.846375
EM: Round [533] log likelihood: -6677.846080
EM: Round [534] log likelihood: -6677.845787
EM: Round [535] log likelihood: -6677.845494
EM: Round [536] log likelihood: -6677.845202
EM: Round [537] log likelihood: -6677.844912
EM: Round [538] log likelihood: -6677.844622
EM: Round [539] log likelihood: -6677.844334
EM: Round [540] log likelihood: -6677.844046
EM: Round [541] log likelihood: -6677.843760
EM: Round [542] log likelihood: -6677.843475
EM: Round [543] log likelihood: -6677.843191
EM: Round [544] log likelihood: -6677.842908
EM: Round [545] log likelihood: -6677.842626
EM: Round [546] log likelihood: -6677.842345
EM: Round [547] log likelihood: -6677.842065
EM: Round [548] log likelihood: -6677.841787
EM: Round [549] log likelihood: -6677.841509
EM: Round [550] log likelihood: -6677.841232
EM: Round [551] log likelihood: -6677.840957
EM: Round [552] log likelihood: -6677.840682
EM: Round [553] log likelihood: -6677.840408
EM: Round [554] log likelihood: -6677.840136
EM: Round [555] log likelihood: -6677.839864
EM: Round [556] log likelihood: -6677.839594
EM: Round [557] log likelihood: -6677.839324
EM: Round [558] log likelihood: -6677.839056
EM: Round [559] log likelihood: -6677.838788
EM: Round [560] log likelihood: -6677.838522
EM: Round [561] log likelihood: -6677.838256
EM: Round [562] log likelihood: -6677.837992
EM: Round [563] log likelihood: -6677.837728
EM: Round [564] log likelihood: -6677.837466
EM: Round [565] log likelihood: -6677.837204
EM: Round [566] log likelihood: -6677.836943
EM: Round [567] log likelihood: -6677.836684
EM: Round [568] log likelihood: -6677.836425
EM: Round [569] log likelihood: -6677.836167
EM: Round [570] log likelihood: -6677.835911
EM: Round [571] log likelihood: -6677.835655
EM: Round [572] log likelihood: -6677.835400
EM: Round [573] log likelihood: -6677.835146
EM: Round [574] log likelihood: -6677.834893
EM: Round [575] log likelihood: -6677.834641
EM: Round [576] log likelihood: -6677.834390
EM: Round [577] log likelihood: -6677.834140
EM: Round [578] log likelihood: -6677.833891
EM: Round [579] log likelihood: -6677.833643
EM: Round [580] log likelihood: -6677.833395
EM: Round [581] log likelihood: -6677.833149
EM: Round [582] log likelihood: -6677.832904
EM: Round [583] log likelihood: -6677.832659
EM: Round [584] log likelihood: -6677.832415
EM: Round [585] log likelihood: -6677.832173
EM: Round [586] log likelihood: -6677.831931
EM: Round [587] log likelihood: -6677.831690
EM: Round [588] log likelihood: -6677.831450
EM: Round [589] log likelihood: -6677.831210
EM: Round [590] log likelihood: -6677.830972
EM: Round [591] log likelihood: -6677.830735
EM: Round [592] log likelihood: -6677.830498
EM: Round [593] log likelihood: -6677.830263
EM: Round [594] log likelihood: -6677.830028
EM: Round [595] log likelihood: -6677.829794
EM: Round [596] log likelihood: -6677.829561
EM: Round [597] log likelihood: -6677.829329
EM: Round [598] log likelihood: -6677.829097
EM: Round [599] log likelihood: -6677.828867
EM: Round [600] log likelihood: -6677.828637
EM: Round [601] log likelihood: -6677.828409
EM: Round [602] log likelihood: -6677.828181
EM: Round [603] log likelihood: -6677.827954
EM: Round [604] log likelihood: -6677.827727
EM: Round [605] log likelihood: -6677.827502
EM: Round [606] log likelihood: -6677.827277
EM: Round [607] log likelihood: -6677.827054
EM: Round [608] log likelihood: -6677.826831
EM: Round [609] log likelihood: -6677.826609
EM: Round [610] log likelihood: -6677.826387
EM: Round [611] log likelihood: -6677.826167
EM: Round [612] log likelihood: -6677.825947
EM: Round [613] log likelihood: -6677.825729
EM: Round [614] log likelihood: -6677.825511
EM: Round [615] log likelihood: -6677.825293
EM: Round [616] log likelihood: -6677.825077
EM: Round [617] log likelihood: -6677.824861
EM: Round [618] log likelihood: -6677.824647
EM: Round [619] log likelihood: -6677.824433
EM: Round [620] log likelihood: -6677.824219
EM: Round [621] log likelihood: -6677.824007
EM: Round [622] log likelihood: -6677.823795
EM: Round [623] log likelihood: -6677.823584
EM: Round [624] log likelihood: -6677.823374
EM: Round [625] log likelihood: -6677.823165
EM: Round [626] log likelihood: -6677.822956
EM: Round [627] log likelihood: -6677.822748
EM: Round [628] log likelihood: -6677.822541
EM: Round [629] log likelihood: -6677.822335
EM: Round [630] log likelihood: -6677.822130
EM: Round [631] log likelihood: -6677.821925
EM: Round [632] log likelihood: -6677.821721
EM: Round [633] log likelihood: -6677.821518
EM: Round [634] log likelihood: -6677.821315
EM: Round [635] log likelihood: -6677.821113
EM: Round [636] log likelihood: -6677.820912
EM: Round [637] log likelihood: -6677.820712
EM: Round [638] log likelihood: -6677.820513
EM: Round [639] log likelihood: -6677.820314
EM: Round [640] log likelihood: -6677.820116
EM: Round [641] log likelihood: -6677.819918
EM: Round [642] log likelihood: -6677.819722
EM: Round [643] log likelihood: -6677.819526
EM: Round [644] log likelihood: -6677.819331
EM: Round [645] log likelihood: -6677.819136
EM: Round [646] log likelihood: -6677.818942
EM: Round [647] log likelihood: -6677.818749
EM: Round [648] log likelihood: -6677.818557
EM: Round [649] log likelihood: -6677.818365
EM: Round [650] log likelihood: -6677.818174
EM: Round [651] log likelihood: -6677.817984
EM: Round [652] log likelihood: -6677.817795
EM: Round [653] log likelihood: -6677.817606
EM: Round [654] log likelihood: -6677.817417
EM: Round [655] log likelihood: -6677.817230
EM: Round [656] log likelihood: -6677.817043
EM: Round [657] log likelihood: -6677.816857
EM: Round [658] log likelihood: -6677.816672
EM: Round [659] log likelihood: -6677.816487
EM: Round [660] log likelihood: -6677.816303
EM: Round [661] log likelihood: -6677.816119
EM: Round [662] log likelihood: -6677.815937
EM: Round [663] log likelihood: -6677.815755
EM: Round [664] log likelihood: -6677.815573
EM: Round [665] log likelihood: -6677.815393
EM: Round [666] log likelihood: -6677.815213
EM: Round [667] log likelihood: -6677.815033
EM: Round [668] log likelihood: -6677.814854
EM: Round [669] log likelihood: -6677.814676
EM: Round [670] log likelihood: -6677.814499
EM: Round [671] log likelihood: -6677.814322
EM: Round [672] log likelihood: -6677.814146
EM: Round [673] log likelihood: -6677.813970
EM: Round [674] log likelihood: -6677.813795
EM: Round [675] log likelihood: -6677.813621
EM: Round [676] log likelihood: -6677.813448
EM: Round [677] log likelihood: -6677.813275
EM: Round [678] log likelihood: -6677.813102
EM: Round [679] log likelihood: -6677.812931
EM: Round [680] log likelihood: -6677.812759
EM: Round [681] log likelihood: -6677.812589
EM: Round [682] log likelihood: -6677.812419
EM: Round [683] log likelihood: -6677.812250
EM: Round [684] log likelihood: -6677.812081
EM: Round [685] log likelihood: -6677.811913
EM: Round [686] log likelihood: -6677.811746
EM: Round [687] log likelihood: -6677.811579
EM: Round [688] log likelihood: -6677.811413
EM: Round [689] log likelihood: -6677.811247
EM: Round [690] log likelihood: -6677.811082
EM: Round [691] log likelihood: -6677.810918
EM: Round [692] log likelihood: -6677.810754
EM: Round [693] log likelihood: -6677.810591
EM: Round [694] log likelihood: -6677.810428
EM: Round [695] log likelihood: -6677.810267
EM: Round [696] log likelihood: -6677.810105
EM: Round [697] log likelihood: -6677.809944
EM: Round [698] log likelihood: -6677.809784
EM: Round [699] log likelihood: -6677.809624
EM: Round [700] log likelihood: -6677.809465
EM: Round [701] log likelihood: -6677.809307
EM: Round [702] log likelihood: -6677.809149
EM: Round [703] log likelihood: -6677.808992
EM: Round [704] log likelihood: -6677.808835
EM: Round [705] log likelihood: -6677.808679
EM: Round [706] log likelihood: -6677.808523
EM: Round [707] log likelihood: -6677.808368
EM: Round [708] log likelihood: -6677.808213
EM: Round [709] log likelihood: -6677.808059
EM: Round [710] log likelihood: -6677.807906
EM: Round [711] log likelihood: -6677.807753
EM: Round [712] log likelihood: -6677.807601
EM: Round [713] log likelihood: -6677.807449
EM: Round [714] log likelihood: -6677.807298
EM: Round [715] log likelihood: -6677.807147
EM: Round [716] log likelihood: -6677.806997
EM: Round [717] log likelihood: -6677.806848
EM: Round [718] log likelihood: -6677.806699
EM: Round [719] log likelihood: -6677.806550
EM: Round [720] log likelihood: -6677.806402
EM: Round [721] log likelihood: -6677.806255
EM: Round [722] log likelihood: -6677.806108
EM: Round [723] log likelihood: -6677.805962
EM: Round [724] log likelihood: -6677.805816
EM: Round [725] log likelihood: -6677.805671
EM: Round [726] log likelihood: -6677.805526
EM: Round [727] log likelihood: -6677.805382
EM: Round [728] log likelihood: -6677.805238
EM: Round [729] log likelihood: -6677.805095
EM: Round [730] log likelihood: -6677.804952
EM: Round [731] log likelihood: -6677.804810
EM: Round [732] log likelihood: -6677.804668
EM: Round [733] log likelihood: -6677.804527
EM: Round [734] log likelihood: -6677.804387
EM: Round [735] log likelihood: -6677.804247
EM: Round [736] log likelihood: -6677.804107
EM: Round [737] log likelihood: -6677.803968
EM: Round [738] log likelihood: -6677.803829
EM: Round [739] log likelihood: -6677.803691
EM: Round [740] log likelihood: -6677.803554
EM: Round [741] log likelihood: -6677.803417
EM: Round [742] log likelihood: -6677.803280
EM: Round [743] log likelihood: -6677.803144
EM: Round [744] log likelihood: -6677.803008
EM: Round [745] log likelihood: -6677.802873
EM: Round [746] log likelihood: -6677.802739
EM: Round [747] log likelihood: -6677.802604
EM: Round [748] log likelihood: -6677.802471
EM: Round [749] log likelihood: -6677.802338
EM: Round [750] log likelihood: -6677.802205
EM: Round [751] log likelihood: -6677.802073
EM: Round [752] log likelihood: -6677.801941
EM: Round [753] log likelihood: -6677.801810
EM: Round [754] log likelihood: -6677.801679
EM: Round [755] log likelihood: -6677.801548
EM: Round [756] log likelihood: -6677.801419
EM: Round [757] log likelihood: -6677.801289
EM: Round [758] log likelihood: -6677.801160
EM: Round [759] log likelihood: -6677.801032
EM: Round [760] log likelihood: -6677.800904
EM: Round [761] log likelihood: -6677.800776
EM: Round [762] log likelihood: -6677.800649
EM: Round [763] log likelihood: -6677.800522
EM: Round [764] log likelihood: -6677.800396
EM: Round [765] log likelihood: -6677.800271
EM: Round [766] log likelihood: -6677.800145
EM: Round [767] log likelihood: -6677.800021
EM: Round [768] log likelihood: -6677.799896
EM: Round [769] log likelihood: -6677.799772
EM: Round [770] log likelihood: -6677.799649
EM: Round [771] log likelihood: -6677.799526
EM: Round [772] log likelihood: -6677.799403
EM: Round [773] log likelihood: -6677.799281
EM: Round [774] log likelihood: -6677.799159
EM: Round [775] log likelihood: -6677.799038
EM: Round [776] log likelihood: -6677.798917
EM: Round [777] log likelihood: -6677.798797
EM: Round [778] log likelihood: -6677.798677
EM: Round [779] log likelihood: -6677.798557
EM: Round [780] log likelihood: -6677.798438
EM: Round [781] log likelihood: -6677.798319
EM: Round [782] log likelihood: -6677.798201
EM: Round [783] log likelihood: -6677.798083
EM: Round [784] log likelihood: -6677.797966
EM: Round [785] log likelihood: -6677.797849
EM: Round [786] log likelihood: -6677.797732
EM: Round [787] log likelihood: -6677.797616
EM: Round [788] log likelihood: -6677.797501
EM: Round [789] log likelihood: -6677.797385
EM: Round [790] log likelihood: -6677.797270
EM: Round [791] log likelihood: -6677.797156
EM: Round [792] log likelihood: -6677.797042
EM: Round [793] log likelihood: -6677.796928
EM: Round [794] log likelihood: -6677.796815
EM: Round [795] log likelihood: -6677.796702
EM: Round [796] log likelihood: -6677.796590
EM: Round [797] log likelihood: -6677.796478
EM: Round [798] log likelihood: -6677.796366
EM: Round [799] log likelihood: -6677.796255
EM: Round [800] log likelihood: -6677.796144
EM: Round [801] log likelihood: -6677.796033
EM: Round [802] log likelihood: -6677.795923
EM: Round [803] log likelihood: -6677.795814
EM: Round [804] log likelihood: -6677.795704
EM: Round [805] log likelihood: -6677.795595
EM: Round [806] log likelihood: -6677.795487
EM: Round [807] log likelihood: -6677.795379
EM: Round [808] log likelihood: -6677.795271
EM: Round [809] log likelihood: -6677.795164
EM: Round [810] log likelihood: -6677.795057
EM: Round [811] log likelihood: -6677.794950
EM: Round [812] log likelihood: -6677.794844
EM: Round [813] log likelihood: -6677.794738
EM: Round [814] log likelihood: -6677.794633
EM: Round [815] log likelihood: -6677.794528
EM: Round [816] log likelihood: -6677.794423
EM: Round [817] log likelihood: -6677.794319
EM: Round [818] log likelihood: -6677.794215
EM: Round [819] log likelihood: -6677.794111
EM: Round [820] log likelihood: -6677.794008
EM: Round [821] log likelihood: -6677.793905
EM: Round [822] log likelihood: -6677.793803
EM: Round [823] log likelihood: -6677.793701
EM: Round [824] log likelihood: -6677.793599
EM: Round [825] log likelihood: -6677.793498
EM: Round [826] log likelihood: -6677.793397
EM: Round [827] log likelihood: -6677.793296
EM: Round [828] log likelihood: -6677.793196
EM: Round [829] log likelihood: -6677.793096
EM: Stopping iterations at round 829 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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 69211967
Execution Time = 1.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gtf > /tmp/nxf.XJibhaNoI4/fi_workdir/microH.dat
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.XJibhaNoI4/fi_workdir/microH.dat /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_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.XJibhaNoI4/fi_workdir/microH.dat /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XJibhaNoI4 --json_outfile /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XJibhaNoI4 --json_outfile /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.XJibhaNoI4/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.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1 --html_output /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1 --html_output /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000242808.10]
WARNING, no entry stored in dbm for [ENSG00000242808.10]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000249375.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XJibhaNoI4/ctat_genome_lib_build_dir > /tmp/nxf.XJibhaNoI4/aih-tih-sc-284856-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.XJibhaNoI4/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory