Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/100443c88505f06c7f057667d466b7/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/100443c88505f06c7f057667d466b7/tih_rna_sample_00637_B23MVV7LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/83eb792d829e9eb95c4c581dd15d64/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/83eb792d829e9eb95c4c581dd15d64/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/17664944aa2ea17a49517f01568047/tih_rna_sample_00637_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00637_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00637_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/cytoBand.txt
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00637_B23MVV7LT4_1.star --out_dir /tmp/nxf.0OGFR4RveV/fi_workdir --reads "/tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:36:33 ..... started STAR run
Jun 08 09:36:33 ..... loading genome
Jun 08 09:38:13 ... generating Suffix Array index
Jun 08 09:41:54 ... completed Suffix Array index
Jun 08 09:41:55 ..... processing annotations GTF
Jun 08 09:41:55 ..... inserting junctions into the genome indices
Jun 08 09:42:56 ..... started mapping
Jun 08 10:26:20 ..... finished mapping
Jun 08 10:26:21 ..... started sorting BAM
Jun 08 10:26:22 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00637_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00637_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 49.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00637_B23MVV7LT4_1.star --out_dir /tmp/nxf.0OGFR4RveV/fi_workdir --reads "/tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:26:32 : INFO : Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1750000] -done parsing /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 241,
'num genes matched < 2' => 77,
'per_id < 96' => 5058,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'low complexity anchor region' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 24,
' ** passed ** ' => 8907,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 171,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 74,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 139,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'excessive soft clipping' => 12185,
'small anchor length' => 6,
'exons hit < 2' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 20
};
-writing fusion junction support info.
Execution Time = 0.95 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[170000] -fusion SPANNING read extraction for scaff: DHX9--MTARC2
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[30000] -fusion SPANNING read extraction for scaff: EFL1--GOLGA6L11P
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[259000] -fusion SPANNING read extraction for scaff: JADE3--KRBOX4
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[18000] -fusion SPANNING read extraction for scaff: KCNQ1--ZNF157
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[33000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[29000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[29000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[28000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC1
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[24000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC2
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[44000] -fusion SPANNING read extraction for scaff: PIP5K1C--TPTEP1
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[42000] -fusion SPANNING read extraction for scaff: PIP5K1C--AP000547.3
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[17000] -fusion SPANNING read extraction for scaff: PPIG--LINC01807
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[17000] -fusion SPANNING read extraction for scaff: PPIG--PID1
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[7000] -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7
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[298000] -fusion SPANNING read extraction for scaff: RBM14--RBM4
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[124000] -fusion SPANNING read extraction for scaff: SFXN5--KNTC1
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[103000] -fusion SPANNING read extraction for scaff: SHANK2--FCHSD2
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[38000] -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 15,
'lacks exon overlap' => 29895
};
Execution Time = 2.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -11282.324638
EM: Round [1] log likelihood: -11282.025662
EM: Round [2] log likelihood: -11282.022578
EM: Round [3] log likelihood: -11282.021025
EM: Round [4] log likelihood: -11282.019507
EM: Round [5] log likelihood: -11282.017995
EM: Round [6] log likelihood: -11282.016491
EM: Round [7] log likelihood: -11282.014993
EM: Round [8] log likelihood: -11282.013502
EM: Round [9] log likelihood: -11282.012019
EM: Round [10] log likelihood: -11282.010542
EM: Round [11] log likelihood: -11282.009071
EM: Round [12] log likelihood: -11282.007608
EM: Round [13] log likelihood: -11282.006151
EM: Round [14] log likelihood: -11282.004700
EM: Round [15] log likelihood: -11282.003257
EM: Round [16] log likelihood: -11282.001819
EM: Round [17] log likelihood: -11282.000389
EM: Round [18] log likelihood: -11281.998964
EM: Round [19] log likelihood: -11281.997547
EM: Round [20] log likelihood: -11281.996135
EM: Round [21] log likelihood: -11281.994730
EM: Round [22] log likelihood: -11281.993331
EM: Round [23] log likelihood: -11281.991939
EM: Round [24] log likelihood: -11281.990552
EM: Round [25] log likelihood: -11281.989172
EM: Round [26] log likelihood: -11281.987798
EM: Round [27] log likelihood: -11281.986431
EM: Round [28] log likelihood: -11281.985069
EM: Round [29] log likelihood: -11281.983713
EM: Round [30] log likelihood: -11281.982364
EM: Round [31] log likelihood: -11281.981020
EM: Round [32] log likelihood: -11281.979683
EM: Round [33] log likelihood: -11281.978351
EM: Round [34] log likelihood: -11281.977025
EM: Round [35] log likelihood: -11281.975705
EM: Round [36] log likelihood: -11281.974391
EM: Round [37] log likelihood: -11281.973082
EM: Round [38] log likelihood: -11281.971780
EM: Round [39] log likelihood: -11281.970483
EM: Round [40] log likelihood: -11281.969192
EM: Round [41] log likelihood: -11281.967906
EM: Round [42] log likelihood: -11281.966626
EM: Round [43] log likelihood: -11281.965352
EM: Round [44] log likelihood: -11281.964083
EM: Round [45] log likelihood: -11281.962820
EM: Round [46] log likelihood: -11281.961562
EM: Round [47] log likelihood: -11281.960310
EM: Round [48] log likelihood: -11281.959063
EM: Round [49] log likelihood: -11281.957821
EM: Round [50] log likelihood: -11281.956585
EM: Round [51] log likelihood: -11281.955355
EM: Round [52] log likelihood: -11281.954129
EM: Round [53] log likelihood: -11281.952909
EM: Round [54] log likelihood: -11281.951694
EM: Round [55] log likelihood: -11281.950484
EM: Round [56] log likelihood: -11281.949280
EM: Round [57] log likelihood: -11281.948081
EM: Round [58] log likelihood: -11281.946887
EM: Round [59] log likelihood: -11281.945698
EM: Round [60] log likelihood: -11281.944514
EM: Round [61] log likelihood: -11281.943335
EM: Round [62] log likelihood: -11281.942161
EM: Round [63] log likelihood: -11281.940992
EM: Round [64] log likelihood: -11281.939828
EM: Round [65] log likelihood: -11281.938669
EM: Round [66] log likelihood: -11281.937515
EM: Round [67] log likelihood: -11281.936366
EM: Round [68] log likelihood: -11281.935222
EM: Round [69] log likelihood: -11281.934083
EM: Round [70] log likelihood: -11281.932948
EM: Round [71] log likelihood: -11281.931818
EM: Round [72] log likelihood: -11281.930693
EM: Round [73] log likelihood: -11281.929573
EM: Round [74] log likelihood: -11281.928457
EM: Round [75] log likelihood: -11281.927347
EM: Round [76] log likelihood: -11281.926240
EM: Round [77] log likelihood: -11281.925139
EM: Round [78] log likelihood: -11281.924042
EM: Round [79] log likelihood: -11281.922950
EM: Round [80] log likelihood: -11281.921862
EM: Round [81] log likelihood: -11281.920779
EM: Round [82] log likelihood: -11281.919700
EM: Round [83] log likelihood: -11281.918626
EM: Round [84] log likelihood: -11281.917556
EM: Round [85] log likelihood: -11281.916491
EM: Round [86] log likelihood: -11281.915430
EM: Round [87] log likelihood: -11281.914373
EM: Round [88] log likelihood: -11281.913321
EM: Round [89] log likelihood: -11281.912273
EM: Round [90] log likelihood: -11281.911230
EM: Round [91] log likelihood: -11281.910191
EM: Round [92] log likelihood: -11281.909156
EM: Round [93] log likelihood: -11281.908126
EM: Round [94] log likelihood: -11281.907099
EM: Round [95] log likelihood: -11281.906077
EM: Round [96] log likelihood: -11281.905060
EM: Round [97] log likelihood: -11281.904046
EM: Round [98] log likelihood: -11281.903036
EM: Round [99] log likelihood: -11281.902031
EM: Round [100] log likelihood: -11281.901030
EM: Round [101] log likelihood: -11281.900033
EM: Round [102] log likelihood: -11281.899040
EM: Round [103] log likelihood: -11281.898051
EM: Round [104] log likelihood: -11281.897066
EM: Round [105] log likelihood: -11281.896085
EM: Round [106] log likelihood: -11281.895108
EM: Round [107] log likelihood: -11281.894135
EM: Round [108] log likelihood: -11281.893166
EM: Round [109] log likelihood: -11281.892201
EM: Round [110] log likelihood: -11281.891239
EM: Round [111] log likelihood: -11281.890282
EM: Round [112] log likelihood: -11281.889329
EM: Round [113] log likelihood: -11281.888379
EM: Round [114] log likelihood: -11281.887433
EM: Round [115] log likelihood: -11281.886491
EM: Round [116] log likelihood: -11281.885553
EM: Round [117] log likelihood: -11281.884619
EM: Round [118] log likelihood: -11281.883688
EM: Round [119] log likelihood: -11281.882762
EM: Round [120] log likelihood: -11281.881838
EM: Round [121] log likelihood: -11281.880919
EM: Round [122] log likelihood: -11281.880003
EM: Round [123] log likelihood: -11281.879091
EM: Round [124] log likelihood: -11281.878183
EM: Round [125] log likelihood: -11281.877278
EM: Round [126] log likelihood: -11281.876377
EM: Round [127] log likelihood: -11281.875479
EM: Round [128] log likelihood: -11281.874585
EM: Round [129] log likelihood: -11281.873695
EM: Round [130] log likelihood: -11281.872808
EM: Round [131] log likelihood: -11281.871925
EM: Round [132] log likelihood: -11281.871045
EM: Round [133] log likelihood: -11281.870169
EM: Round [134] log likelihood: -11281.869296
EM: Round [135] log likelihood: -11281.868426
EM: Round [136] log likelihood: -11281.867560
EM: Round [137] log likelihood: -11281.866698
EM: Round [138] log likelihood: -11281.865839
EM: Round [139] log likelihood: -11281.864983
EM: Round [140] log likelihood: -11281.864131
EM: Round [141] log likelihood: -11281.863282
EM: Round [142] log likelihood: -11281.862436
EM: Round [143] log likelihood: -11281.861594
EM: Round [144] log likelihood: -11281.860755
EM: Round [145] log likelihood: -11281.859919
EM: Round [146] log likelihood: -11281.859087
EM: Round [147] log likelihood: -11281.858258
EM: Round [148] log likelihood: -11281.857432
EM: Round [149] log likelihood: -11281.856609
EM: Round [150] log likelihood: -11281.855790
EM: Round [151] log likelihood: -11281.854973
EM: Round [152] log likelihood: -11281.854160
EM: Round [153] log likelihood: -11281.853350
EM: Round [154] log likelihood: -11281.852544
EM: Round [155] log likelihood: -11281.851740
EM: Round [156] log likelihood: -11281.850940
EM: Round [157] log likelihood: -11281.850142
EM: Round [158] log likelihood: -11281.849348
EM: Round [159] log likelihood: -11281.848557
EM: Round [160] log likelihood: -11281.847769
EM: Round [161] log likelihood: -11281.846984
EM: Round [162] log likelihood: -11281.846202
EM: Round [163] log likelihood: -11281.845423
EM: Round [164] log likelihood: -11281.844647
EM: Round [165] log likelihood: -11281.843874
EM: Round [166] log likelihood: -11281.843104
EM: Round [167] log likelihood: -11281.842337
EM: Round [168] log likelihood: -11281.841573
EM: Round [169] log likelihood: -11281.840812
EM: Round [170] log likelihood: -11281.840054
EM: Round [171] log likelihood: -11281.839299
EM: Round [172] log likelihood: -11281.838547
EM: Round [173] log likelihood: -11281.837797
EM: Round [174] log likelihood: -11281.837051
EM: Round [175] log likelihood: -11281.836307
EM: Round [176] log likelihood: -11281.835566
EM: Round [177] log likelihood: -11281.834828
EM: Round [178] log likelihood: -11281.834093
EM: Round [179] log likelihood: -11281.833361
EM: Round [180] log likelihood: -11281.832631
EM: Round [181] log likelihood: -11281.831905
EM: Round [182] log likelihood: -11281.831181
EM: Round [183] log likelihood: -11281.830459
EM: Round [184] log likelihood: -11281.829741
EM: Round [185] log likelihood: -11281.829025
EM: Round [186] log likelihood: -11281.828312
EM: Round [187] log likelihood: -11281.827602
EM: Round [188] log likelihood: -11281.826894
EM: Round [189] log likelihood: -11281.826189
EM: Round [190] log likelihood: -11281.825487
EM: Round [191] log likelihood: -11281.824788
EM: Round [192] log likelihood: -11281.824091
EM: Round [193] log likelihood: -11281.823397
EM: Round [194] log likelihood: -11281.822705
EM: Round [195] log likelihood: -11281.822016
EM: Round [196] log likelihood: -11281.821330
EM: Round [197] log likelihood: -11281.820646
EM: Round [198] log likelihood: -11281.819965
EM: Round [199] log likelihood: -11281.819286
EM: Round [200] log likelihood: -11281.818610
EM: Round [201] log likelihood: -11281.817936
EM: Round [202] log likelihood: -11281.817265
EM: Round [203] log likelihood: -11281.816597
EM: Round [204] log likelihood: -11281.815931
EM: Round [205] log likelihood: -11281.815267
EM: Round [206] log likelihood: -11281.814606
EM: Round [207] log likelihood: -11281.813948
EM: Round [208] log likelihood: -11281.813292
EM: Round [209] log likelihood: -11281.812638
EM: Round [210] log likelihood: -11281.811987
EM: Round [211] log likelihood: -11281.811338
EM: Round [212] log likelihood: -11281.810692
EM: Round [213] log likelihood: -11281.810048
EM: Round [214] log likelihood: -11281.809407
EM: Round [215] log likelihood: -11281.808768
EM: Round [216] log likelihood: -11281.808131
EM: Round [217] log likelihood: -11281.807497
EM: Round [218] log likelihood: -11281.806865
EM: Round [219] log likelihood: -11281.806235
EM: Round [220] log likelihood: -11281.805608
EM: Round [221] log likelihood: -11281.804983
EM: Round [222] log likelihood: -11281.804361
EM: Round [223] log likelihood: -11281.803741
EM: Round [224] log likelihood: -11281.803123
EM: Round [225] log likelihood: -11281.802507
EM: Round [226] log likelihood: -11281.801894
EM: Round [227] log likelihood: -11281.801282
EM: Round [228] log likelihood: -11281.800674
EM: Round [229] log likelihood: -11281.800067
EM: Round [230] log likelihood: -11281.799463
EM: Round [231] log likelihood: -11281.798861
EM: Round [232] log likelihood: -11281.798261
EM: Round [233] log likelihood: -11281.797663
EM: Round [234] log likelihood: -11281.797068
EM: Round [235] log likelihood: -11281.796474
EM: Round [236] log likelihood: -11281.795883
EM: Round [237] log likelihood: -11281.795294
EM: Round [238] log likelihood: -11281.794708
EM: Round [239] log likelihood: -11281.794123
EM: Round [240] log likelihood: -11281.793541
EM: Round [241] log likelihood: -11281.792960
EM: Round [242] log likelihood: -11281.792382
EM: Round [243] log likelihood: -11281.791806
EM: Round [244] log likelihood: -11281.791232
EM: Round [245] log likelihood: -11281.790661
EM: Round [246] log likelihood: -11281.790091
EM: Round [247] log likelihood: -11281.789523
EM: Round [248] log likelihood: -11281.788958
EM: Round [249] log likelihood: -11281.788394
EM: Round [250] log likelihood: -11281.787833
EM: Round [251] log likelihood: -11281.787273
EM: Round [252] log likelihood: -11281.786716
EM: Round [253] log likelihood: -11281.786161
EM: Round [254] log likelihood: -11281.785608
EM: Round [255] log likelihood: -11281.785056
EM: Round [256] log likelihood: -11281.784507
EM: Round [257] log likelihood: -11281.783960
EM: Round [258] log likelihood: -11281.783415
EM: Round [259] log likelihood: -11281.782871
EM: Round [260] log likelihood: -11281.782330
EM: Round [261] log likelihood: -11281.781791
EM: Round [262] log likelihood: -11281.781253
EM: Round [263] log likelihood: -11281.780718
EM: Round [264] log likelihood: -11281.780185
EM: Round [265] log likelihood: -11281.779653
EM: Round [266] log likelihood: -11281.779123
EM: Round [267] log likelihood: -11281.778596
EM: Round [268] log likelihood: -11281.778070
EM: Round [269] log likelihood: -11281.777546
EM: Round [270] log likelihood: -11281.777024
EM: Round [271] log likelihood: -11281.776504
EM: Round [272] log likelihood: -11281.775986
EM: Round [273] log likelihood: -11281.775469
EM: Round [274] log likelihood: -11281.774955
EM: Round [275] log likelihood: -11281.774442
EM: Round [276] log likelihood: -11281.773932
EM: Round [277] log likelihood: -11281.773423
EM: Round [278] log likelihood: -11281.772916
EM: Round [279] log likelihood: -11281.772410
EM: Round [280] log likelihood: -11281.771907
EM: Round [281] log likelihood: -11281.771405
EM: Round [282] log likelihood: -11281.770905
EM: Round [283] log likelihood: -11281.770407
EM: Round [284] log likelihood: -11281.769911
EM: Round [285] log likelihood: -11281.769417
EM: Round [286] log likelihood: -11281.768924
EM: Round [287] log likelihood: -11281.768433
EM: Round [288] log likelihood: -11281.767944
EM: Round [289] log likelihood: -11281.767456
EM: Round [290] log likelihood: -11281.766971
EM: Round [291] log likelihood: -11281.766487
EM: Round [292] log likelihood: -11281.766005
EM: Round [293] log likelihood: -11281.765524
EM: Round [294] log likelihood: -11281.765045
EM: Round [295] log likelihood: -11281.764568
EM: Round [296] log likelihood: -11281.764093
EM: Round [297] log likelihood: -11281.763619
EM: Round [298] log likelihood: -11281.763147
EM: Round [299] log likelihood: -11281.762677
EM: Round [300] log likelihood: -11281.762209
EM: Round [301] log likelihood: -11281.761742
EM: Round [302] log likelihood: -11281.761276
EM: Round [303] log likelihood: -11281.760813
EM: Round [304] log likelihood: -11281.760351
EM: Round [305] log likelihood: -11281.759890
EM: Round [306] log likelihood: -11281.759432
EM: Round [307] log likelihood: -11281.758975
EM: Round [308] log likelihood: -11281.758519
EM: Round [309] log likelihood: -11281.758065
EM: Round [310] log likelihood: -11281.757613
EM: Round [311] log likelihood: -11281.757163
EM: Round [312] log likelihood: -11281.756714
EM: Round [313] log likelihood: -11281.756266
EM: Round [314] log likelihood: -11281.755820
EM: Round [315] log likelihood: -11281.755376
EM: Round [316] log likelihood: -11281.754933
EM: Round [317] log likelihood: -11281.754492
EM: Round [318] log likelihood: -11281.754053
EM: Round [319] log likelihood: -11281.753615
EM: Round [320] log likelihood: -11281.753178
EM: Round [321] log likelihood: -11281.752743
EM: Round [322] log likelihood: -11281.752310
EM: Round [323] log likelihood: -11281.751878
EM: Round [324] log likelihood: -11281.751448
EM: Round [325] log likelihood: -11281.751019
EM: Round [326] log likelihood: -11281.750592
EM: Round [327] log likelihood: -11281.750166
EM: Round [328] log likelihood: -11281.749742
EM: Round [329] log likelihood: -11281.749319
EM: Round [330] log likelihood: -11281.748897
EM: Round [331] log likelihood: -11281.748478
EM: Round [332] log likelihood: -11281.748059
EM: Round [333] log likelihood: -11281.747642
EM: Round [334] log likelihood: -11281.747227
EM: Round [335] log likelihood: -11281.746813
EM: Round [336] log likelihood: -11281.746400
EM: Round [337] log likelihood: -11281.745989
EM: Round [338] log likelihood: -11281.745580
EM: Round [339] log likelihood: -11281.745172
EM: Round [340] log likelihood: -11281.744765
EM: Round [341] log likelihood: -11281.744359
EM: Round [342] log likelihood: -11281.743956
EM: Round [343] log likelihood: -11281.743553
EM: Round [344] log likelihood: -11281.743152
EM: Round [345] log likelihood: -11281.742752
EM: Round [346] log likelihood: -11281.742354
EM: Round [347] log likelihood: -11281.741957
EM: Round [348] log likelihood: -11281.741561
EM: Round [349] log likelihood: -11281.741167
EM: Round [350] log likelihood: -11281.740775
EM: Round [351] log likelihood: -11281.740383
EM: Round [352] log likelihood: -11281.739993
EM: Round [353] log likelihood: -11281.739604
EM: Round [354] log likelihood: -11281.739217
EM: Round [355] log likelihood: -11281.738831
EM: Round [356] log likelihood: -11281.738446
EM: Round [357] log likelihood: -11281.738063
EM: Round [358] log likelihood: -11281.737681
EM: Round [359] log likelihood: -11281.737301
EM: Round [360] log likelihood: -11281.736921
EM: Round [361] log likelihood: -11281.736543
EM: Round [362] log likelihood: -11281.736167
EM: Round [363] log likelihood: -11281.735791
EM: Round [364] log likelihood: -11281.735417
EM: Round [365] log likelihood: -11281.735044
EM: Round [366] log likelihood: -11281.734673
EM: Round [367] log likelihood: -11281.734303
EM: Round [368] log likelihood: -11281.733934
EM: Round [369] log likelihood: -11281.733566
EM: Round [370] log likelihood: -11281.733200
EM: Round [371] log likelihood: -11281.732835
EM: Round [372] log likelihood: -11281.732471
EM: Round [373] log likelihood: -11281.732108
EM: Round [374] log likelihood: -11281.731747
EM: Round [375] log likelihood: -11281.731387
EM: Round [376] log likelihood: -11281.731028
EM: Round [377] log likelihood: -11281.730670
EM: Round [378] log likelihood: -11281.730314
EM: Round [379] log likelihood: -11281.729959
EM: Round [380] log likelihood: -11281.729605
EM: Round [381] log likelihood: -11281.729252
EM: Round [382] log likelihood: -11281.728901
EM: Round [383] log likelihood: -11281.728551
EM: Round [384] log likelihood: -11281.728201
EM: Round [385] log likelihood: -11281.727854
EM: Round [386] log likelihood: -11281.727507
EM: Round [387] log likelihood: -11281.727162
EM: Round [388] log likelihood: -11281.726817
EM: Round [389] log likelihood: -11281.726474
EM: Round [390] log likelihood: -11281.726132
EM: Round [391] log likelihood: -11281.725792
EM: Round [392] log likelihood: -11281.725452
EM: Round [393] log likelihood: -11281.725114
EM: Round [394] log likelihood: -11281.724776
EM: Round [395] log likelihood: -11281.724440
EM: Round [396] log likelihood: -11281.724105
EM: Round [397] log likelihood: -11281.723772
EM: Round [398] log likelihood: -11281.723439
EM: Round [399] log likelihood: -11281.723107
EM: Round [400] log likelihood: -11281.722777
EM: Round [401] log likelihood: -11281.722448
EM: Round [402] log likelihood: -11281.722120
EM: Round [403] log likelihood: -11281.721793
EM: Round [404] log likelihood: -11281.721467
EM: Round [405] log likelihood: -11281.721142
EM: Round [406] log likelihood: -11281.720819
EM: Round [407] log likelihood: -11281.720496
EM: Round [408] log likelihood: -11281.720175
EM: Round [409] log likelihood: -11281.719854
EM: Round [410] log likelihood: -11281.719535
EM: Round [411] log likelihood: -11281.719217
EM: Round [412] log likelihood: -11281.718900
EM: Round [413] log likelihood: -11281.718584
EM: Round [414] log likelihood: -11281.718269
EM: Round [415] log likelihood: -11281.717955
EM: Round [416] log likelihood: -11281.717642
EM: Round [417] log likelihood: -11281.717331
EM: Round [418] log likelihood: -11281.717020
EM: Round [419] log likelihood: -11281.716710
EM: Round [420] log likelihood: -11281.716402
EM: Round [421] log likelihood: -11281.716095
EM: Round [422] log likelihood: -11281.715788
EM: Round [423] log likelihood: -11281.715483
EM: Round [424] log likelihood: -11281.715178
EM: Round [425] log likelihood: -11281.714875
EM: Round [426] log likelihood: -11281.714573
EM: Round [427] log likelihood: -11281.714272
EM: Round [428] log likelihood: -11281.713971
EM: Round [429] log likelihood: -11281.713672
EM: Round [430] log likelihood: -11281.713374
EM: Round [431] log likelihood: -11281.713077
EM: Round [432] log likelihood: -11281.712781
EM: Round [433] log likelihood: -11281.712485
EM: Round [434] log likelihood: -11281.712191
EM: Round [435] log likelihood: -11281.711898
EM: Round [436] log likelihood: -11281.711606
EM: Round [437] log likelihood: -11281.711315
EM: Round [438] log likelihood: -11281.711025
EM: Round [439] log likelihood: -11281.710735
EM: Round [440] log likelihood: -11281.710447
EM: Round [441] log likelihood: -11281.710160
EM: Round [442] log likelihood: -11281.709873
EM: Round [443] log likelihood: -11281.709588
EM: Round [444] log likelihood: -11281.709304
EM: Round [445] log likelihood: -11281.709020
EM: Round [446] log likelihood: -11281.708738
EM: Round [447] log likelihood: -11281.708456
EM: Round [448] log likelihood: -11281.708176
EM: Round [449] log likelihood: -11281.707896
EM: Round [450] log likelihood: -11281.707618
EM: Round [451] log likelihood: -11281.707340
EM: Round [452] log likelihood: -11281.707063
EM: Round [453] log likelihood: -11281.706787
EM: Round [454] log likelihood: -11281.706512
EM: Round [455] log likelihood: -11281.706238
EM: Round [456] log likelihood: -11281.705965
EM: Round [457] log likelihood: -11281.705693
EM: Round [458] log likelihood: -11281.705422
EM: Round [459] log likelihood: -11281.705152
EM: Round [460] log likelihood: -11281.704882
EM: Round [461] log likelihood: -11281.704614
EM: Round [462] log likelihood: -11281.704346
EM: Round [463] log likelihood: -11281.704080
EM: Round [464] log likelihood: -11281.703814
EM: Round [465] log likelihood: -11281.703549
EM: Round [466] log likelihood: -11281.703285
EM: Round [467] log likelihood: -11281.703022
EM: Round [468] log likelihood: -11281.702760
EM: Round [469] log likelihood: -11281.702498
EM: Round [470] log likelihood: -11281.702238
EM: Round [471] log likelihood: -11281.701978
EM: Round [472] log likelihood: -11281.701719
EM: Round [473] log likelihood: -11281.701461
EM: Round [474] log likelihood: -11281.701204
EM: Round [475] log likelihood: -11281.700948
EM: Round [476] log likelihood: -11281.700693
EM: Round [477] log likelihood: -11281.700439
EM: Round [478] log likelihood: -11281.700185
EM: Round [479] log likelihood: -11281.699932
EM: Round [480] log likelihood: -11281.699680
EM: Round [481] log likelihood: -11281.699429
EM: Round [482] log likelihood: -11281.699179
EM: Round [483] log likelihood: -11281.698930
EM: Round [484] log likelihood: -11281.698681
EM: Round [485] log likelihood: -11281.698434
EM: Round [486] log likelihood: -11281.698187
EM: Round [487] log likelihood: -11281.697941
EM: Round [488] log likelihood: -11281.697695
EM: Round [489] log likelihood: -11281.697451
EM: Round [490] log likelihood: -11281.697207
EM: Round [491] log likelihood: -11281.696965
EM: Round [492] log likelihood: -11281.696723
EM: Round [493] log likelihood: -11281.696481
EM: Round [494] log likelihood: -11281.696241
EM: Round [495] log likelihood: -11281.696002
EM: Round [496] log likelihood: -11281.695763
EM: Round [497] log likelihood: -11281.695525
EM: Round [498] log likelihood: -11281.695288
EM: Round [499] log likelihood: -11281.695051
EM: Round [500] log likelihood: -11281.694816
EM: Round [501] log likelihood: -11281.694581
EM: Round [502] log likelihood: -11281.694347
EM: Round [503] log likelihood: -11281.694114
EM: Round [504] log likelihood: -11281.693881
EM: Round [505] log likelihood: -11281.693649
EM: Round [506] log likelihood: -11281.693419
EM: Round [507] log likelihood: -11281.693188
EM: Round [508] log likelihood: -11281.692959
EM: Round [509] log likelihood: -11281.692730
EM: Round [510] log likelihood: -11281.692503
EM: Round [511] log likelihood: -11281.692275
EM: Round [512] log likelihood: -11281.692049
EM: Round [513] log likelihood: -11281.691823
EM: Round [514] log likelihood: -11281.691599
EM: Round [515] log likelihood: -11281.691374
EM: Round [516] log likelihood: -11281.691151
EM: Round [517] log likelihood: -11281.690929
EM: Round [518] log likelihood: -11281.690707
EM: Round [519] log likelihood: -11281.690485
EM: Round [520] log likelihood: -11281.690265
EM: Round [521] log likelihood: -11281.690045
EM: Round [522] log likelihood: -11281.689826
EM: Round [523] log likelihood: -11281.689608
EM: Round [524] log likelihood: -11281.689391
EM: Round [525] log likelihood: -11281.689174
EM: Round [526] log likelihood: -11281.688958
EM: Round [527] log likelihood: -11281.688742
EM: Round [528] log likelihood: -11281.688528
EM: Round [529] log likelihood: -11281.688314
EM: Round [530] log likelihood: -11281.688101
EM: Round [531] log likelihood: -11281.687888
EM: Round [532] log likelihood: -11281.687676
EM: Round [533] log likelihood: -11281.687465
EM: Round [534] log likelihood: -11281.687255
EM: Round [535] log likelihood: -11281.687045
EM: Round [536] log likelihood: -11281.686836
EM: Round [537] log likelihood: -11281.686628
EM: Round [538] log likelihood: -11281.686420
EM: Round [539] log likelihood: -11281.686213
EM: Round [540] log likelihood: -11281.686007
EM: Round [541] log likelihood: -11281.685801
EM: Round [542] log likelihood: -11281.685596
EM: Round [543] log likelihood: -11281.685392
EM: Round [544] log likelihood: -11281.685189
EM: Round [545] log likelihood: -11281.684986
EM: Round [546] log likelihood: -11281.684783
EM: Round [547] log likelihood: -11281.684582
EM: Round [548] log likelihood: -11281.684381
EM: Round [549] log likelihood: -11281.684181
EM: Round [550] log likelihood: -11281.683981
EM: Round [551] log likelihood: -11281.683782
EM: Round [552] log likelihood: -11281.683584
EM: Round [553] log likelihood: -11281.683386
EM: Round [554] log likelihood: -11281.683189
EM: Round [555] log likelihood: -11281.682993
EM: Round [556] log likelihood: -11281.682797
EM: Round [557] log likelihood: -11281.682602
EM: Round [558] log likelihood: -11281.682408
EM: Round [559] log likelihood: -11281.682214
EM: Round [560] log likelihood: -11281.682021
EM: Round [561] log likelihood: -11281.681829
EM: Round [562] log likelihood: -11281.681637
EM: Round [563] log likelihood: -11281.681446
EM: Round [564] log likelihood: -11281.681255
EM: Round [565] log likelihood: -11281.681065
EM: Round [566] log likelihood: -11281.680876
EM: Round [567] log likelihood: -11281.680687
EM: Round [568] log likelihood: -11281.680499
EM: Round [569] log likelihood: -11281.680312
EM: Round [570] log likelihood: -11281.680125
EM: Round [571] log likelihood: -11281.679938
EM: Round [572] log likelihood: -11281.679753
EM: Round [573] log likelihood: -11281.679568
EM: Round [574] log likelihood: -11281.679383
EM: Round [575] log likelihood: -11281.679200
EM: Round [576] log likelihood: -11281.679016
EM: Round [577] log likelihood: -11281.678834
EM: Round [578] log likelihood: -11281.678652
EM: Round [579] log likelihood: -11281.678470
EM: Round [580] log likelihood: -11281.678290
EM: Round [581] log likelihood: -11281.678109
EM: Round [582] log likelihood: -11281.677930
EM: Round [583] log likelihood: -11281.677751
EM: Round [584] log likelihood: -11281.677572
EM: Round [585] log likelihood: -11281.677394
EM: Round [586] log likelihood: -11281.677217
EM: Round [587] log likelihood: -11281.677040
EM: Round [588] log likelihood: -11281.676864
EM: Round [589] log likelihood: -11281.676689
EM: Round [590] log likelihood: -11281.676514
EM: Round [591] log likelihood: -11281.676339
EM: Round [592] log likelihood: -11281.676165
EM: Round [593] log likelihood: -11281.675992
EM: Round [594] log likelihood: -11281.675819
EM: Round [595] log likelihood: -11281.675647
EM: Round [596] log likelihood: -11281.675476
EM: Round [597] log likelihood: -11281.675305
EM: Round [598] log likelihood: -11281.675134
EM: Round [599] log likelihood: -11281.674964
EM: Round [600] log likelihood: -11281.674795
EM: Round [601] log likelihood: -11281.674626
EM: Round [602] log likelihood: -11281.674458
EM: Round [603] log likelihood: -11281.674290
EM: Round [604] log likelihood: -11281.674123
EM: Round [605] log likelihood: -11281.673956
EM: Round [606] log likelihood: -11281.673790
EM: Round [607] log likelihood: -11281.673625
EM: Round [608] log likelihood: -11281.673460
EM: Round [609] log likelihood: -11281.673295
EM: Round [610] log likelihood: -11281.673132
EM: Round [611] log likelihood: -11281.672968
EM: Round [612] log likelihood: -11281.672805
EM: Round [613] log likelihood: -11281.672643
EM: Round [614] log likelihood: -11281.672481
EM: Round [615] log likelihood: -11281.672320
EM: Round [616] log likelihood: -11281.672159
EM: Round [617] log likelihood: -11281.671999
EM: Round [618] log likelihood: -11281.671839
EM: Round [619] log likelihood: -11281.671680
EM: Round [620] log likelihood: -11281.671522
EM: Round [621] log likelihood: -11281.671363
EM: Round [622] log likelihood: -11281.671206
EM: Round [623] log likelihood: -11281.671049
EM: Round [624] log likelihood: -11281.670892
EM: Round [625] log likelihood: -11281.670736
EM: Round [626] log likelihood: -11281.670581
EM: Round [627] log likelihood: -11281.670425
EM: Round [628] log likelihood: -11281.670271
EM: Round [629] log likelihood: -11281.670117
EM: Round [630] log likelihood: -11281.669963
EM: Round [631] log likelihood: -11281.669810
EM: Round [632] log likelihood: -11281.669658
EM: Round [633] log likelihood: -11281.669506
EM: Round [634] log likelihood: -11281.669354
EM: Round [635] log likelihood: -11281.669203
EM: Round [636] log likelihood: -11281.669052
EM: Round [637] log likelihood: -11281.668902
EM: Round [638] log likelihood: -11281.668753
EM: Round [639] log likelihood: -11281.668603
EM: Round [640] log likelihood: -11281.668455
EM: Round [641] log likelihood: -11281.668307
EM: Round [642] log likelihood: -11281.668159
EM: Round [643] log likelihood: -11281.668012
EM: Round [644] log likelihood: -11281.667865
EM: Round [645] log likelihood: -11281.667719
EM: Round [646] log likelihood: -11281.667573
EM: Round [647] log likelihood: -11281.667428
EM: Round [648] log likelihood: -11281.667283
EM: Round [649] log likelihood: -11281.667139
EM: Round [650] log likelihood: -11281.666995
EM: Round [651] log likelihood: -11281.666851
EM: Round [652] log likelihood: -11281.666708
EM: Round [653] log likelihood: -11281.666566
EM: Round [654] log likelihood: -11281.666424
EM: Round [655] log likelihood: -11281.666282
EM: Round [656] log likelihood: -11281.666141
EM: Round [657] log likelihood: -11281.666000
EM: Round [658] log likelihood: -11281.665860
EM: Round [659] log likelihood: -11281.665720
EM: Round [660] log likelihood: -11281.665581
EM: Round [661] log likelihood: -11281.665442
EM: Round [662] log likelihood: -11281.665304
EM: Round [663] log likelihood: -11281.665166
EM: Round [664] log likelihood: -11281.665028
EM: Round [665] log likelihood: -11281.664891
EM: Round [666] log likelihood: -11281.664755
EM: Round [667] log likelihood: -11281.664618
EM: Round [668] log likelihood: -11281.664483
EM: Round [669] log likelihood: -11281.664347
EM: Round [670] log likelihood: -11281.664212
EM: Round [671] log likelihood: -11281.664078
EM: Round [672] log likelihood: -11281.663944
EM: Round [673] log likelihood: -11281.663810
EM: Round [674] log likelihood: -11281.663677
EM: Round [675] log likelihood: -11281.663545
EM: Round [676] log likelihood: -11281.663412
EM: Round [677] log likelihood: -11281.663281
EM: Round [678] log likelihood: -11281.663149
EM: Round [679] log likelihood: -11281.663018
EM: Round [680] log likelihood: -11281.662888
EM: Round [681] log likelihood: -11281.662757
EM: Round [682] log likelihood: -11281.662628
EM: Round [683] log likelihood: -11281.662498
EM: Round [684] log likelihood: -11281.662369
EM: Round [685] log likelihood: -11281.662241
EM: Round [686] log likelihood: -11281.662113
EM: Round [687] log likelihood: -11281.661985
EM: Round [688] log likelihood: -11281.661858
EM: Round [689] log likelihood: -11281.661731
EM: Round [690] log likelihood: -11281.661605
EM: Round [691] log likelihood: -11281.661479
EM: Round [692] log likelihood: -11281.661353
EM: Round [693] log likelihood: -11281.661228
EM: Round [694] log likelihood: -11281.661103
EM: Round [695] log likelihood: -11281.660979
EM: Round [696] log likelihood: -11281.660855
EM: Round [697] log likelihood: -11281.660731
EM: Round [698] log likelihood: -11281.660608
EM: Round [699] log likelihood: -11281.660485
EM: Round [700] log likelihood: -11281.660363
EM: Round [701] log likelihood: -11281.660241
EM: Round [702] log likelihood: -11281.660119
EM: Round [703] log likelihood: -11281.659998
EM: Round [704] log likelihood: -11281.659877
EM: Round [705] log likelihood: -11281.659756
EM: Round [706] log likelihood: -11281.659636
EM: Round [707] log likelihood: -11281.659517
EM: Round [708] log likelihood: -11281.659397
EM: Round [709] log likelihood: -11281.659278
EM: Round [710] log likelihood: -11281.659160
EM: Round [711] log likelihood: -11281.659042
EM: Round [712] log likelihood: -11281.658924
EM: Round [713] log likelihood: -11281.658807
EM: Round [714] log likelihood: -11281.658690
EM: Round [715] log likelihood: -11281.658573
EM: Round [716] log likelihood: -11281.658457
EM: Round [717] log likelihood: -11281.658341
EM: Round [718] log likelihood: -11281.658225
EM: Round [719] log likelihood: -11281.658110
EM: Round [720] log likelihood: -11281.657995
EM: Round [721] log likelihood: -11281.657881
EM: Round [722] log likelihood: -11281.657767
EM: Round [723] log likelihood: -11281.657653
EM: Round [724] log likelihood: -11281.657540
EM: Round [725] log likelihood: -11281.657427
EM: Round [726] log likelihood: -11281.657314
EM: Round [727] log likelihood: -11281.657202
EM: Round [728] log likelihood: -11281.657090
EM: Round [729] log likelihood: -11281.656979
EM: Round [730] log likelihood: -11281.656868
EM: Round [731] log likelihood: -11281.656757
EM: Round [732] log likelihood: -11281.656646
EM: Round [733] log likelihood: -11281.656536
EM: Round [734] log likelihood: -11281.656426
EM: Round [735] log likelihood: -11281.656317
EM: Round [736] log likelihood: -11281.656208
EM: Round [737] log likelihood: -11281.656099
EM: Round [738] log likelihood: -11281.655991
EM: Round [739] log likelihood: -11281.655883
EM: Round [740] log likelihood: -11281.655775
EM: Round [741] log likelihood: -11281.655668
EM: Round [742] log likelihood: -11281.655561
EM: Round [743] log likelihood: -11281.655455
EM: Round [744] log likelihood: -11281.655348
EM: Round [745] log likelihood: -11281.655242
EM: Round [746] log likelihood: -11281.655137
EM: Round [747] log likelihood: -11281.655032
EM: Round [748] log likelihood: -11281.654927
EM: Round [749] log likelihood: -11281.654822
EM: Round [750] log likelihood: -11281.654718
EM: Round [751] log likelihood: -11281.654614
EM: Round [752] log likelihood: -11281.654510
EM: Round [753] log likelihood: -11281.654407
EM: Round [754] log likelihood: -11281.654304
EM: Round [755] log likelihood: -11281.654202
EM: Round [756] log likelihood: -11281.654099
EM: Round [757] log likelihood: -11281.653997
EM: Round [758] log likelihood: -11281.653896
EM: Round [759] log likelihood: -11281.653794
EM: Round [760] log likelihood: -11281.653694
EM: Round [761] log likelihood: -11281.653593
EM: Round [762] log likelihood: -11281.653493
EM: Round [763] log likelihood: -11281.653393
EM: Stopping iterations at round 763 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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/tih_rna_sample_00637_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa > /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.0OGFR4RveV/fi_workdir/tih_rna_sample_00637_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir
-done, see /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -8594.663573
EM: Round [1] log likelihood: -8594.510930
EM: Round [2] log likelihood: -8594.506328
EM: Round [3] log likelihood: -8594.503267
EM: Round [4] log likelihood: -8594.500250
EM: Round [5] log likelihood: -8594.497253
EM: Round [6] log likelihood: -8594.494273
EM: Round [7] log likelihood: -8594.491312
EM: Round [8] log likelihood: -8594.488368
EM: Round [9] log likelihood: -8594.485442
EM: Round [10] log likelihood: -8594.482534
EM: Round [11] log likelihood: -8594.479643
EM: Round [12] log likelihood: -8594.476769
EM: Round [13] log likelihood: -8594.473913
EM: Round [14] log likelihood: -8594.471073
EM: Round [15] log likelihood: -8594.468250
EM: Round [16] log likelihood: -8594.465444
EM: Round [17] log likelihood: -8594.462655
EM: Round [18] log likelihood: -8594.459881
EM: Round [19] log likelihood: -8594.457124
EM: Round [20] log likelihood: -8594.454383
EM: Round [21] log likelihood: -8594.451658
EM: Round [22] log likelihood: -8594.448949
EM: Round [23] log likelihood: -8594.446255
EM: Round [24] log likelihood: -8594.443577
EM: Round [25] log likelihood: -8594.440915
EM: Round [26] log likelihood: -8594.438267
EM: Round [27] log likelihood: -8594.435635
EM: Round [28] log likelihood: -8594.433018
EM: Round [29] log likelihood: -8594.430416
EM: Round [30] log likelihood: -8594.427828
EM: Round [31] log likelihood: -8594.425255
EM: Round [32] log likelihood: -8594.422697
EM: Round [33] log likelihood: -8594.420153
EM: Round [34] log likelihood: -8594.417624
EM: Round [35] log likelihood: -8594.415108
EM: Round [36] log likelihood: -8594.412607
EM: Round [37] log likelihood: -8594.410120
EM: Round [38] log likelihood: -8594.407646
EM: Round [39] log likelihood: -8594.405186
EM: Round [40] log likelihood: -8594.402740
EM: Round [41] log likelihood: -8594.400308
EM: Round [42] log likelihood: -8594.397888
EM: Round [43] log likelihood: -8594.395482
EM: Round [44] log likelihood: -8594.393090
EM: Round [45] log likelihood: -8594.390710
EM: Round [46] log likelihood: -8594.388343
EM: Round [47] log likelihood: -8594.385990
EM: Round [48] log likelihood: -8594.383649
EM: Round [49] log likelihood: -8594.381320
EM: Round [50] log likelihood: -8594.379005
EM: Round [51] log likelihood: -8594.376702
EM: Round [52] log likelihood: -8594.374411
EM: Round [53] log likelihood: -8594.372132
EM: Round [54] log likelihood: -8594.369866
EM: Round [55] log likelihood: -8594.367612
EM: Round [56] log likelihood: -8594.365370
EM: Round [57] log likelihood: -8594.363139
EM: Round [58] log likelihood: -8594.360921
EM: Round [59] log likelihood: -8594.358714
EM: Round [60] log likelihood: -8594.356520
EM: Round [61] log likelihood: -8594.354336
EM: Round [62] log likelihood: -8594.352164
EM: Round [63] log likelihood: -8594.350004
EM: Round [64] log likelihood: -8594.347855
EM: Round [65] log likelihood: -8594.345717
EM: Round [66] log likelihood: -8594.343590
EM: Round [67] log likelihood: -8594.341474
EM: Round [68] log likelihood: -8594.339370
EM: Round [69] log likelihood: -8594.337276
EM: Round [70] log likelihood: -8594.335193
EM: Round [71] log likelihood: -8594.333121
EM: Round [72] log likelihood: -8594.331059
EM: Round [73] log likelihood: -8594.329009
EM: Round [74] log likelihood: -8594.326968
EM: Round [75] log likelihood: -8594.324938
EM: Round [76] log likelihood: -8594.322919
EM: Round [77] log likelihood: -8594.320910
EM: Round [78] log likelihood: -8594.318911
EM: Round [79] log likelihood: -8594.316922
EM: Round [80] log likelihood: -8594.314943
EM: Round [81] log likelihood: -8594.312974
EM: Round [82] log likelihood: -8594.311016
EM: Round [83] log likelihood: -8594.309067
EM: Round [84] log likelihood: -8594.307128
EM: Round [85] log likelihood: -8594.305198
EM: Round [86] log likelihood: -8594.303279
EM: Round [87] log likelihood: -8594.301369
EM: Round [88] log likelihood: -8594.299468
EM: Round [89] log likelihood: -8594.297577
EM: Round [90] log likelihood: -8594.295695
EM: Round [91] log likelihood: -8594.293823
EM: Round [92] log likelihood: -8594.291960
EM: Round [93] log likelihood: -8594.290106
EM: Round [94] log likelihood: -8594.288261
EM: Round [95] log likelihood: -8594.286426
EM: Round [96] log likelihood: -8594.284599
EM: Round [97] log likelihood: -8594.282782
EM: Round [98] log likelihood: -8594.280973
EM: Round [99] log likelihood: -8594.279173
EM: Round [100] log likelihood: -8594.277382
EM: Round [101] log likelihood: -8594.275600
EM: Round [102] log likelihood: -8594.273826
EM: Round [103] log likelihood: -8594.272061
EM: Round [104] log likelihood: -8594.270305
EM: Round [105] log likelihood: -8594.268557
EM: Round [106] log likelihood: -8594.266818
EM: Round [107] log likelihood: -8594.265086
EM: Round [108] log likelihood: -8594.263364
EM: Round [109] log likelihood: -8594.261649
EM: Round [110] log likelihood: -8594.259943
EM: Round [111] log likelihood: -8594.258245
EM: Round [112] log likelihood: -8594.256555
EM: Round [113] log likelihood: -8594.254873
EM: Round [114] log likelihood: -8594.253199
EM: Round [115] log likelihood: -8594.251533
EM: Round [116] log likelihood: -8594.249875
EM: Round [117] log likelihood: -8594.248225
EM: Round [118] log likelihood: -8594.246583
EM: Round [119] log likelihood: -8594.244948
EM: Round [120] log likelihood: -8594.243322
EM: Round [121] log likelihood: -8594.241702
EM: Round [122] log likelihood: -8594.240091
EM: Round [123] log likelihood: -8594.238487
EM: Round [124] log likelihood: -8594.236890
EM: Round [125] log likelihood: -8594.235302
EM: Round [126] log likelihood: -8594.233720
EM: Round [127] log likelihood: -8594.232146
EM: Round [128] log likelihood: -8594.230579
EM: Round [129] log likelihood: -8594.229019
EM: Round [130] log likelihood: -8594.227467
EM: Round [131] log likelihood: -8594.225922
EM: Round [132] log likelihood: -8594.224384
EM: Round [133] log likelihood: -8594.222853
EM: Round [134] log likelihood: -8594.221330
EM: Round [135] log likelihood: -8594.219813
EM: Round [136] log likelihood: -8594.218303
EM: Round [137] log likelihood: -8594.216800
EM: Round [138] log likelihood: -8594.215304
EM: Round [139] log likelihood: -8594.213815
EM: Round [140] log likelihood: -8594.212333
EM: Round [141] log likelihood: -8594.210858
EM: Round [142] log likelihood: -8594.209389
EM: Round [143] log likelihood: -8594.207927
EM: Round [144] log likelihood: -8594.206472
EM: Round [145] log likelihood: -8594.205023
EM: Round [146] log likelihood: -8594.203581
EM: Round [147] log likelihood: -8594.202145
EM: Round [148] log likelihood: -8594.200716
EM: Round [149] log likelihood: -8594.199293
EM: Round [150] log likelihood: -8594.197877
EM: Round [151] log likelihood: -8594.196467
EM: Round [152] log likelihood: -8594.195063
EM: Round [153] log likelihood: -8594.193666
EM: Round [154] log likelihood: -8594.192275
EM: Round [155] log likelihood: -8594.190890
EM: Round [156] log likelihood: -8594.189511
EM: Round [157] log likelihood: -8594.188139
EM: Round [158] log likelihood: -8594.186773
EM: Round [159] log likelihood: -8594.185412
EM: Round [160] log likelihood: -8594.184058
EM: Round [161] log likelihood: -8594.182710
EM: Round [162] log likelihood: -8594.181368
EM: Round [163] log likelihood: -8594.180032
EM: Round [164] log likelihood: -8594.178701
EM: Round [165] log likelihood: -8594.177377
EM: Round [166] log likelihood: -8594.176058
EM: Round [167] log likelihood: -8594.174746
EM: Round [168] log likelihood: -8594.173439
EM: Round [169] log likelihood: -8594.172137
EM: Round [170] log likelihood: -8594.170842
EM: Round [171] log likelihood: -8594.169552
EM: Round [172] log likelihood: -8594.168268
EM: Round [173] log likelihood: -8594.166989
EM: Round [174] log likelihood: -8594.165716
EM: Round [175] log likelihood: -8594.164448
EM: Round [176] log likelihood: -8594.163186
EM: Round [177] log likelihood: -8594.161930
EM: Round [178] log likelihood: -8594.160679
EM: Round [179] log likelihood: -8594.159433
EM: Round [180] log likelihood: -8594.158193
EM: Round [181] log likelihood: -8594.156958
EM: Round [182] log likelihood: -8594.155729
EM: Round [183] log likelihood: -8594.154505
EM: Round [184] log likelihood: -8594.153286
EM: Round [185] log likelihood: -8594.152072
EM: Round [186] log likelihood: -8594.150864
EM: Round [187] log likelihood: -8594.149661
EM: Round [188] log likelihood: -8594.148463
EM: Round [189] log likelihood: -8594.147270
EM: Round [190] log likelihood: -8594.146082
EM: Round [191] log likelihood: -8594.144899
EM: Round [192] log likelihood: -8594.143721
EM: Round [193] log likelihood: -8594.142549
EM: Round [194] log likelihood: -8594.141381
EM: Round [195] log likelihood: -8594.140218
EM: Round [196] log likelihood: -8594.139061
EM: Round [197] log likelihood: -8594.137908
EM: Round [198] log likelihood: -8594.136760
EM: Round [199] log likelihood: -8594.135617
EM: Round [200] log likelihood: -8594.134479
EM: Round [201] log likelihood: -8594.133345
EM: Round [202] log likelihood: -8594.132217
EM: Round [203] log likelihood: -8594.131093
EM: Round [204] log likelihood: -8594.129974
EM: Round [205] log likelihood: -8594.128859
EM: Round [206] log likelihood: -8594.127749
EM: Round [207] log likelihood: -8594.126644
EM: Round [208] log likelihood: -8594.125544
EM: Round [209] log likelihood: -8594.124448
EM: Round [210] log likelihood: -8594.123357
EM: Round [211] log likelihood: -8594.122270
EM: Round [212] log likelihood: -8594.121188
EM: Round [213] log likelihood: -8594.120110
EM: Round [214] log likelihood: -8594.119037
EM: Round [215] log likelihood: -8594.117968
EM: Round [216] log likelihood: -8594.116904
EM: Round [217] log likelihood: -8594.115844
EM: Round [218] log likelihood: -8594.114789
EM: Round [219] log likelihood: -8594.113738
EM: Round [220] log likelihood: -8594.112691
EM: Round [221] log likelihood: -8594.111649
EM: Round [222] log likelihood: -8594.110611
EM: Round [223] log likelihood: -8594.109577
EM: Round [224] log likelihood: -8594.108548
EM: Round [225] log likelihood: -8594.107522
EM: Round [226] log likelihood: -8594.106501
EM: Round [227] log likelihood: -8594.105484
EM: Round [228] log likelihood: -8594.104472
EM: Round [229] log likelihood: -8594.103463
EM: Round [230] log likelihood: -8594.102459
EM: Round [231] log likelihood: -8594.101459
EM: Round [232] log likelihood: -8594.100462
EM: Round [233] log likelihood: -8594.099470
EM: Round [234] log likelihood: -8594.098482
EM: Round [235] log likelihood: -8594.097498
EM: Round [236] log likelihood: -8594.096518
EM: Round [237] log likelihood: -8594.095542
EM: Round [238] log likelihood: -8594.094570
EM: Round [239] log likelihood: -8594.093602
EM: Round [240] log likelihood: -8594.092638
EM: Round [241] log likelihood: -8594.091678
EM: Round [242] log likelihood: -8594.090721
EM: Round [243] log likelihood: -8594.089769
EM: Round [244] log likelihood: -8594.088820
EM: Round [245] log likelihood: -8594.087875
EM: Round [246] log likelihood: -8594.086934
EM: Round [247] log likelihood: -8594.085997
EM: Round [248] log likelihood: -8594.085064
EM: Round [249] log likelihood: -8594.084134
EM: Round [250] log likelihood: -8594.083208
EM: Round [251] log likelihood: -8594.082286
EM: Round [252] log likelihood: -8594.081367
EM: Round [253] log likelihood: -8594.080452
EM: Round [254] log likelihood: -8594.079541
EM: Round [255] log likelihood: -8594.078634
EM: Round [256] log likelihood: -8594.077730
EM: Round [257] log likelihood: -8594.076829
EM: Round [258] log likelihood: -8594.075933
EM: Round [259] log likelihood: -8594.075040
EM: Round [260] log likelihood: -8594.074150
EM: Round [261] log likelihood: -8594.073264
EM: Round [262] log likelihood: -8594.072382
EM: Round [263] log likelihood: -8594.071503
EM: Round [264] log likelihood: -8594.070627
EM: Round [265] log likelihood: -8594.069755
EM: Round [266] log likelihood: -8594.068886
EM: Round [267] log likelihood: -8594.068021
EM: Round [268] log likelihood: -8594.067160
EM: Round [269] log likelihood: -8594.066301
EM: Round [270] log likelihood: -8594.065446
EM: Round [271] log likelihood: -8594.064595
EM: Round [272] log likelihood: -8594.063747
EM: Round [273] log likelihood: -8594.062902
EM: Round [274] log likelihood: -8594.062060
EM: Round [275] log likelihood: -8594.061222
EM: Round [276] log likelihood: -8594.060387
EM: Round [277] log likelihood: -8594.059556
EM: Round [278] log likelihood: -8594.058727
EM: Round [279] log likelihood: -8594.057902
EM: Round [280] log likelihood: -8594.057080
EM: Round [281] log likelihood: -8594.056261
EM: Round [282] log likelihood: -8594.055446
EM: Round [283] log likelihood: -8594.054634
EM: Round [284] log likelihood: -8594.053825
EM: Round [285] log likelihood: -8594.053019
EM: Round [286] log likelihood: -8594.052216
EM: Round [287] log likelihood: -8594.051416
EM: Round [288] log likelihood: -8594.050619
EM: Round [289] log likelihood: -8594.049826
EM: Round [290] log likelihood: -8594.049036
EM: Round [291] log likelihood: -8594.048248
EM: Round [292] log likelihood: -8594.047464
EM: Round [293] log likelihood: -8594.046683
EM: Round [294] log likelihood: -8594.045905
EM: Round [295] log likelihood: -8594.045129
EM: Round [296] log likelihood: -8594.044357
EM: Round [297] log likelihood: -8594.043588
EM: Round [298] log likelihood: -8594.042822
EM: Round [299] log likelihood: -8594.042058
EM: Round [300] log likelihood: -8594.041298
EM: Round [301] log likelihood: -8594.040541
EM: Round [302] log likelihood: -8594.039786
EM: Round [303] log likelihood: -8594.039034
EM: Round [304] log likelihood: -8594.038286
EM: Round [305] log likelihood: -8594.037540
EM: Round [306] log likelihood: -8594.036797
EM: Round [307] log likelihood: -8594.036057
EM: Round [308] log likelihood: -8594.035319
EM: Round [309] log likelihood: -8594.034585
EM: Round [310] log likelihood: -8594.033853
EM: Round [311] log likelihood: -8594.033124
EM: Round [312] log likelihood: -8594.032398
EM: Round [313] log likelihood: -8594.031675
EM: Round [314] log likelihood: -8594.030955
EM: Round [315] log likelihood: -8594.030237
EM: Round [316] log likelihood: -8594.029522
EM: Round [317] log likelihood: -8594.028809
EM: Round [318] log likelihood: -8594.028100
EM: Round [319] log likelihood: -8594.027393
EM: Round [320] log likelihood: -8594.026688
EM: Round [321] log likelihood: -8594.025987
EM: Round [322] log likelihood: -8594.025288
EM: Round [323] log likelihood: -8594.024592
EM: Round [324] log likelihood: -8594.023898
EM: Round [325] log likelihood: -8594.023207
EM: Round [326] log likelihood: -8594.022519
EM: Round [327] log likelihood: -8594.021833
EM: Round [328] log likelihood: -8594.021150
EM: Round [329] log likelihood: -8594.020469
EM: Round [330] log likelihood: -8594.019791
EM: Round [331] log likelihood: -8594.019116
EM: Round [332] log likelihood: -8594.018443
EM: Round [333] log likelihood: -8594.017772
EM: Round [334] log likelihood: -8594.017104
EM: Round [335] log likelihood: -8594.016439
EM: Round [336] log likelihood: -8594.015776
EM: Round [337] log likelihood: -8594.015116
EM: Round [338] log likelihood: -8594.014458
EM: Round [339] log likelihood: -8594.013802
EM: Round [340] log likelihood: -8594.013149
EM: Round [341] log likelihood: -8594.012499
EM: Round [342] log likelihood: -8594.011851
EM: Round [343] log likelihood: -8594.011205
EM: Round [344] log likelihood: -8594.010562
EM: Round [345] log likelihood: -8594.009921
EM: Round [346] log likelihood: -8594.009282
EM: Round [347] log likelihood: -8594.008646
EM: Round [348] log likelihood: -8594.008013
EM: Round [349] log likelihood: -8594.007381
EM: Round [350] log likelihood: -8594.006752
EM: Round [351] log likelihood: -8594.006126
EM: Round [352] log likelihood: -8594.005501
EM: Round [353] log likelihood: -8594.004879
EM: Round [354] log likelihood: -8594.004260
EM: Round [355] log likelihood: -8594.003642
EM: Round [356] log likelihood: -8594.003027
EM: Round [357] log likelihood: -8594.002414
EM: Round [358] log likelihood: -8594.001804
EM: Round [359] log likelihood: -8594.001195
EM: Round [360] log likelihood: -8594.000589
EM: Round [361] log likelihood: -8593.999986
EM: Round [362] log likelihood: -8593.999384
EM: Round [363] log likelihood: -8593.998785
EM: Round [364] log likelihood: -8593.998188
EM: Round [365] log likelihood: -8593.997593
EM: Round [366] log likelihood: -8593.997000
EM: Round [367] log likelihood: -8593.996409
EM: Round [368] log likelihood: -8593.995821
EM: Round [369] log likelihood: -8593.995235
EM: Round [370] log likelihood: -8593.994651
EM: Round [371] log likelihood: -8593.994069
EM: Round [372] log likelihood: -8593.993489
EM: Round [373] log likelihood: -8593.992911
EM: Round [374] log likelihood: -8593.992336
EM: Round [375] log likelihood: -8593.991762
EM: Round [376] log likelihood: -8593.991191
EM: Round [377] log likelihood: -8593.990622
EM: Round [378] log likelihood: -8593.990055
EM: Round [379] log likelihood: -8593.989490
EM: Round [380] log likelihood: -8593.988927
EM: Round [381] log likelihood: -8593.988366
EM: Round [382] log likelihood: -8593.987807
EM: Round [383] log likelihood: -8593.987250
EM: Round [384] log likelihood: -8593.986695
EM: Round [385] log likelihood: -8593.986143
EM: Round [386] log likelihood: -8593.985592
EM: Round [387] log likelihood: -8593.985043
EM: Round [388] log likelihood: -8593.984496
EM: Round [389] log likelihood: -8593.983951
EM: Round [390] log likelihood: -8593.983409
EM: Round [391] log likelihood: -8593.982868
EM: Round [392] log likelihood: -8593.982329
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EM: Round [847] log likelihood: -8593.859095
EM: Round [848] log likelihood: -8593.858979
EM: Round [849] log likelihood: -8593.858864
EM: Round [850] log likelihood: -8593.858749
EM: Round [851] log likelihood: -8593.858634
EM: Round [852] log likelihood: -8593.858520
EM: Round [853] log likelihood: -8593.858406
EM: Round [854] log likelihood: -8593.858292
EM: Round [855] log likelihood: -8593.858179
EM: Round [856] log likelihood: -8593.858066
EM: Round [857] log likelihood: -8593.857954
EM: Round [858] log likelihood: -8593.857842
EM: Round [859] log likelihood: -8593.857730
EM: Round [860] log likelihood: -8593.857618
EM: Round [861] log likelihood: -8593.857507
EM: Round [862] log likelihood: -8593.857397
EM: Round [863] log likelihood: -8593.857286
EM: Round [864] log likelihood: -8593.857176
EM: Round [865] log likelihood: -8593.857067
EM: Round [866] log likelihood: -8593.856957
EM: Round [867] log likelihood: -8593.856848
EM: Round [868] log likelihood: -8593.856740
EM: Round [869] log likelihood: -8593.856631
EM: Round [870] log likelihood: -8593.856524
EM: Round [871] log likelihood: -8593.856416
EM: Round [872] log likelihood: -8593.856309
EM: Round [873] log likelihood: -8593.856202
EM: Round [874] log likelihood: -8593.856095
EM: Round [875] log likelihood: -8593.855989
EM: Round [876] log likelihood: -8593.855883
EM: Round [877] log likelihood: -8593.855778
EM: Round [878] log likelihood: -8593.855673
EM: Round [879] log likelihood: -8593.855568
EM: Round [880] log likelihood: -8593.855463
EM: Round [881] log likelihood: -8593.855359
EM: Round [882] log likelihood: -8593.855255
EM: Round [883] log likelihood: -8593.855152
EM: Round [884] log likelihood: -8593.855049
EM: Round [885] log likelihood: -8593.854946
EM: Round [886] log likelihood: -8593.854843
EM: Round [887] log likelihood: -8593.854741
EM: Round [888] log likelihood: -8593.854639
EM: Round [889] log likelihood: -8593.854538
EM: Round [890] log likelihood: -8593.854437
EM: Round [891] log likelihood: -8593.854336
EM: Round [892] log likelihood: -8593.854235
EM: Round [893] log likelihood: -8593.854135
EM: Round [894] log likelihood: -8593.854035
EM: Stopping iterations at round 894 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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz: 260811201
Execution Time = 4.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa --gtf /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fa --gtf /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gtf > /tmp/nxf.0OGFR4RveV/fi_workdir/microH.dat
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.0OGFR4RveV/fi_workdir/microH.dat /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.0OGFR4RveV/fi_workdir/microH.dat /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.0OGFR4RveV --json_outfile /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00637_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.0OGFR4RveV --json_outfile /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00637_B23MVV7LT4_1
Running: touch /tmp/nxf.0OGFR4RveV/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.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00637_B23MVV7LT4_1 --html_output /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00637_B23MVV7LT4_1 --html_output /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
WARNING, no entry stored in dbm for [ENSG00000283633.1]
WARNING, no entry stored in dbm for [ENSG00000283633.1]
WARNING, no entry stored in dbm for [ENSG00000283633.1]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000222017.1]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
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]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.0OGFR4RveV/ctat_genome_lib_build_dir > /tmp/nxf.0OGFR4RveV/tih_rna_sample_00637_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.0OGFR4RveV/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory