Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/215d0cff7c5980cbb2204a5606af9e/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_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/fe/97216b9d939ae0ea29ef1b5f534a08/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/b4196fd342343076b959926fd33e11/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/97216b9d939ae0ea29ef1b5f534a08/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/215d0cff7c5980cbb2204a5606af9e/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/cytoBand.txt
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.Wyv1hwOhSd/fi_workdir --reads "/tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:34:19 ..... started STAR run
Jun 08 10:34:19 ..... loading genome
Jun 08 10:35:57 ... generating Suffix Array index
Jun 08 10:39:40 ... completed Suffix Array index
Jun 08 10:39:41 ..... processing annotations GTF
Jun 08 10:39:41 ..... inserting junctions into the genome indices
Jun 08 10:40:41 ..... started mapping
Jun 08 11:28:38 ..... finished mapping
Jun 08 11:28:39 ..... started sorting BAM
Jun 08 11:28:40 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 54.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.Wyv1hwOhSd/fi_workdir --reads "/tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
11:28:54 : INFO : Done.
Execution Time = 0.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[2660000] -done parsing /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 5,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 27,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
'excessive soft clipping' => 19424,
'per_id < 96' => 13648,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 24,
'num genes matched < 2' => 102,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 48,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
' ** passed ** ' => 2895,
'low complexity anchor region' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72,
'small anchor length' => 36
};
-writing fusion junction support info.
Execution Time = 1.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[180000] -fusion SPANNING read extraction for scaff: COX19--SNX8
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[81000] -fusion SPANNING read extraction for scaff: DNAAF5--AC009412.1
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[81000] -fusion SPANNING read extraction for scaff: DNAAF5--FAM220A
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[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 19654,
'seq similar region alignment' => 10799
};
Execution Time = 3.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2175.656447
EM: Round [1] log likelihood: -2175.642364
EM: Round [2] log likelihood: -2175.628479
EM: Round [3] log likelihood: -2175.614789
EM: Round [4] log likelihood: -2175.601289
EM: Round [5] log likelihood: -2175.587975
EM: Round [6] log likelihood: -2175.574843
EM: Round [7] log likelihood: -2175.561891
EM: Round [8] log likelihood: -2175.549113
EM: Round [9] log likelihood: -2175.536508
EM: Round [10] log likelihood: -2175.524071
EM: Round [11] log likelihood: -2175.511799
EM: Round [12] log likelihood: -2175.499689
EM: Round [13] log likelihood: -2175.487739
EM: Round [14] log likelihood: -2175.475944
EM: Round [15] log likelihood: -2175.464302
EM: Round [16] log likelihood: -2175.452810
EM: Round [17] log likelihood: -2175.441465
EM: Round [18] log likelihood: -2175.430265
EM: Round [19] log likelihood: -2175.419207
EM: Round [20] log likelihood: -2175.408289
EM: Round [21] log likelihood: -2175.397507
EM: Round [22] log likelihood: -2175.386860
EM: Round [23] log likelihood: -2175.376345
EM: Round [24] log likelihood: -2175.365960
EM: Round [25] log likelihood: -2175.355702
EM: Round [26] log likelihood: -2175.345570
EM: Round [27] log likelihood: -2175.335561
EM: Round [28] log likelihood: -2175.325673
EM: Round [29] log likelihood: -2175.315903
EM: Round [30] log likelihood: -2175.306251
EM: Round [31] log likelihood: -2175.296714
EM: Round [32] log likelihood: -2175.287290
EM: Round [33] log likelihood: -2175.277978
EM: Round [34] log likelihood: -2175.268774
EM: Round [35] log likelihood: -2175.259679
EM: Round [36] log likelihood: -2175.250689
EM: Round [37] log likelihood: -2175.241804
EM: Round [38] log likelihood: -2175.233021
EM: Round [39] log likelihood: -2175.224339
EM: Round [40] log likelihood: -2175.215757
EM: Round [41] log likelihood: -2175.207272
EM: Round [42] log likelihood: -2175.198884
EM: Round [43] log likelihood: -2175.190590
EM: Round [44] log likelihood: -2175.182390
EM: Round [45] log likelihood: -2175.174281
EM: Round [46] log likelihood: -2175.166264
EM: Round [47] log likelihood: -2175.158335
EM: Round [48] log likelihood: -2175.150494
EM: Round [49] log likelihood: -2175.142740
EM: Round [50] log likelihood: -2175.135070
EM: Round [51] log likelihood: -2175.127485
EM: Round [52] log likelihood: -2175.119983
EM: Round [53] log likelihood: -2175.112562
EM: Round [54] log likelihood: -2175.105221
EM: Round [55] log likelihood: -2175.097960
EM: Round [56] log likelihood: -2175.090776
EM: Round [57] log likelihood: -2175.083670
EM: Round [58] log likelihood: -2175.076639
EM: Round [59] log likelihood: -2175.069683
EM: Round [60] log likelihood: -2175.062801
EM: Round [61] log likelihood: -2175.055991
EM: Round [62] log likelihood: -2175.049254
EM: Round [63] log likelihood: -2175.042586
EM: Round [64] log likelihood: -2175.035989
EM: Round [65] log likelihood: -2175.029460
EM: Round [66] log likelihood: -2175.022999
EM: Round [67] log likelihood: -2175.016606
EM: Round [68] log likelihood: -2175.010278
EM: Round [69] log likelihood: -2175.004015
EM: Round [70] log likelihood: -2174.997816
EM: Round [71] log likelihood: -2174.991681
EM: Round [72] log likelihood: -2174.985608
EM: Round [73] log likelihood: -2174.979597
EM: Round [74] log likelihood: -2174.973647
EM: Round [75] log likelihood: -2174.967757
EM: Round [76] log likelihood: -2174.961926
EM: Round [77] log likelihood: -2174.956154
EM: Round [78] log likelihood: -2174.950440
EM: Round [79] log likelihood: -2174.944783
EM: Round [80] log likelihood: -2174.939182
EM: Round [81] log likelihood: -2174.933637
EM: Round [82] log likelihood: -2174.928146
EM: Round [83] log likelihood: -2174.922710
EM: Round [84] log likelihood: -2174.917328
EM: Round [85] log likelihood: -2174.911998
EM: Round [86] log likelihood: -2174.906721
EM: Round [87] log likelihood: -2174.901495
EM: Round [88] log likelihood: -2174.896320
EM: Round [89] log likelihood: -2174.891195
EM: Round [90] log likelihood: -2174.886120
EM: Round [91] log likelihood: -2174.881094
EM: Round [92] log likelihood: -2174.876117
EM: Round [93] log likelihood: -2174.871188
EM: Round [94] log likelihood: -2174.866305
EM: Round [95] log likelihood: -2174.861470
EM: Round [96] log likelihood: -2174.856681
EM: Round [97] log likelihood: -2174.851937
EM: Round [98] log likelihood: -2174.847239
EM: Round [99] log likelihood: -2174.842585
EM: Round [100] log likelihood: -2174.837975
EM: Round [101] log likelihood: -2174.833409
EM: Round [102] log likelihood: -2174.828886
EM: Round [103] log likelihood: -2174.824405
EM: Round [104] log likelihood: -2174.819966
EM: Round [105] log likelihood: -2174.815569
EM: Round [106] log likelihood: -2174.811213
EM: Round [107] log likelihood: -2174.806898
EM: Round [108] log likelihood: -2174.802622
EM: Round [109] log likelihood: -2174.798387
EM: Round [110] log likelihood: -2174.794190
EM: Round [111] log likelihood: -2174.790032
EM: Round [112] log likelihood: -2174.785913
EM: Round [113] log likelihood: -2174.781832
EM: Round [114] log likelihood: -2174.777788
EM: Round [115] log likelihood: -2174.773781
EM: Round [116] log likelihood: -2174.769810
EM: Round [117] log likelihood: -2174.765876
EM: Round [118] log likelihood: -2174.761978
EM: Round [119] log likelihood: -2174.758115
EM: Round [120] log likelihood: -2174.754288
EM: Round [121] log likelihood: -2174.750495
EM: Round [122] log likelihood: -2174.746736
EM: Round [123] log likelihood: -2174.743011
EM: Round [124] log likelihood: -2174.739320
EM: Round [125] log likelihood: -2174.735662
EM: Round [126] log likelihood: -2174.732037
EM: Round [127] log likelihood: -2174.728444
EM: Round [128] log likelihood: -2174.724883
EM: Round [129] log likelihood: -2174.721355
EM: Round [130] log likelihood: -2174.717857
EM: Round [131] log likelihood: -2174.714391
EM: Round [132] log likelihood: -2174.710955
EM: Round [133] log likelihood: -2174.707550
EM: Round [134] log likelihood: -2174.704175
EM: Round [135] log likelihood: -2174.700830
EM: Round [136] log likelihood: -2174.697515
EM: Round [137] log likelihood: -2174.694228
EM: Round [138] log likelihood: -2174.690971
EM: Round [139] log likelihood: -2174.687742
EM: Round [140] log likelihood: -2174.684541
EM: Round [141] log likelihood: -2174.681369
EM: Round [142] log likelihood: -2174.678224
EM: Round [143] log likelihood: -2174.675106
EM: Round [144] log likelihood: -2174.672016
EM: Round [145] log likelihood: -2174.668953
EM: Round [146] log likelihood: -2174.665916
EM: Round [147] log likelihood: -2174.662905
EM: Round [148] log likelihood: -2174.659921
EM: Round [149] log likelihood: -2174.656962
EM: Round [150] log likelihood: -2174.654029
EM: Round [151] log likelihood: -2174.651121
EM: Round [152] log likelihood: -2174.648238
EM: Round [153] log likelihood: -2174.645380
EM: Round [154] log likelihood: -2174.642546
EM: Round [155] log likelihood: -2174.639737
EM: Round [156] log likelihood: -2174.636952
EM: Round [157] log likelihood: -2174.634190
EM: Round [158] log likelihood: -2174.631453
EM: Round [159] log likelihood: -2174.628738
EM: Round [160] log likelihood: -2174.626047
EM: Round [161] log likelihood: -2174.623378
EM: Round [162] log likelihood: -2174.620732
EM: Round [163] log likelihood: -2174.618109
EM: Round [164] log likelihood: -2174.615507
EM: Round [165] log likelihood: -2174.612928
EM: Round [166] log likelihood: -2174.610370
EM: Round [167] log likelihood: -2174.607834
EM: Round [168] log likelihood: -2174.605320
EM: Round [169] log likelihood: -2174.602826
EM: Round [170] log likelihood: -2174.600354
EM: Round [171] log likelihood: -2174.597902
EM: Round [172] log likelihood: -2174.595471
EM: Round [173] log likelihood: -2174.593060
EM: Round [174] log likelihood: -2174.590669
EM: Round [175] log likelihood: -2174.588298
EM: Round [176] log likelihood: -2174.585947
EM: Round [177] log likelihood: -2174.583616
EM: Round [178] log likelihood: -2174.581304
EM: Round [179] log likelihood: -2174.579011
EM: Round [180] log likelihood: -2174.576737
EM: Round [181] log likelihood: -2174.574482
EM: Round [182] log likelihood: -2174.572246
EM: Round [183] log likelihood: -2174.570028
EM: Round [184] log likelihood: -2174.567829
EM: Round [185] log likelihood: -2174.565648
EM: Round [186] log likelihood: -2174.563485
EM: Round [187] log likelihood: -2174.561339
EM: Round [188] log likelihood: -2174.559211
EM: Round [189] log likelihood: -2174.557101
EM: Round [190] log likelihood: -2174.555008
EM: Round [191] log likelihood: -2174.552932
EM: Round [192] log likelihood: -2174.550873
EM: Round [193] log likelihood: -2174.548831
EM: Round [194] log likelihood: -2174.546806
EM: Round [195] log likelihood: -2174.544798
EM: Round [196] log likelihood: -2174.542805
EM: Round [197] log likelihood: -2174.540829
EM: Round [198] log likelihood: -2174.538869
EM: Round [199] log likelihood: -2174.536925
EM: Round [200] log likelihood: -2174.534997
EM: Round [201] log likelihood: -2174.533084
EM: Round [202] log likelihood: -2174.531187
EM: Round [203] log likelihood: -2174.529306
EM: Round [204] log likelihood: -2174.527439
EM: Round [205] log likelihood: -2174.525588
EM: Round [206] log likelihood: -2174.523752
EM: Round [207] log likelihood: -2174.521930
EM: Round [208] log likelihood: -2174.520123
EM: Round [209] log likelihood: -2174.518331
EM: Round [210] log likelihood: -2174.516553
EM: Round [211] log likelihood: -2174.514790
EM: Round [212] log likelihood: -2174.513040
EM: Round [213] log likelihood: -2174.511305
EM: Round [214] log likelihood: -2174.509584
EM: Round [215] log likelihood: -2174.507876
EM: Round [216] log likelihood: -2174.506182
EM: Round [217] log likelihood: -2174.504502
EM: Round [218] log likelihood: -2174.502835
EM: Round [219] log likelihood: -2174.501181
EM: Round [220] log likelihood: -2174.499541
EM: Round [221] log likelihood: -2174.497914
EM: Round [222] log likelihood: -2174.496299
EM: Round [223] log likelihood: -2174.494698
EM: Round [224] log likelihood: -2174.493109
EM: Round [225] log likelihood: -2174.491533
EM: Round [226] log likelihood: -2174.489970
EM: Round [227] log likelihood: -2174.488419
EM: Round [228] log likelihood: -2174.486880
EM: Round [229] log likelihood: -2174.485353
EM: Round [230] log likelihood: -2174.483839
EM: Round [231] log likelihood: -2174.482336
EM: Round [232] log likelihood: -2174.480846
EM: Round [233] log likelihood: -2174.479367
EM: Round [234] log likelihood: -2174.477900
EM: Round [235] log likelihood: -2174.476444
EM: Round [236] log likelihood: -2174.475000
EM: Round [237] log likelihood: -2174.473567
EM: Round [238] log likelihood: -2174.472146
EM: Round [239] log likelihood: -2174.470736
EM: Round [240] log likelihood: -2174.469336
EM: Round [241] log likelihood: -2174.467948
EM: Round [242] log likelihood: -2174.466571
EM: Round [243] log likelihood: -2174.465205
EM: Round [244] log likelihood: -2174.463849
EM: Round [245] log likelihood: -2174.462504
EM: Round [246] log likelihood: -2174.461169
EM: Round [247] log likelihood: -2174.459845
EM: Round [248] log likelihood: -2174.458531
EM: Round [249] log likelihood: -2174.457228
EM: Round [250] log likelihood: -2174.455935
EM: Round [251] log likelihood: -2174.454651
EM: Round [252] log likelihood: -2174.453378
EM: Round [253] log likelihood: -2174.452115
EM: Round [254] log likelihood: -2174.450862
EM: Round [255] log likelihood: -2174.449618
EM: Round [256] log likelihood: -2174.448384
EM: Round [257] log likelihood: -2174.447160
EM: Round [258] log likelihood: -2174.445945
EM: Round [259] log likelihood: -2174.444739
EM: Round [260] log likelihood: -2174.443543
EM: Round [261] log likelihood: -2174.442356
EM: Round [262] log likelihood: -2174.441179
EM: Round [263] log likelihood: -2174.440010
EM: Round [264] log likelihood: -2174.438851
EM: Round [265] log likelihood: -2174.437701
EM: Round [266] log likelihood: -2174.436559
EM: Round [267] log likelihood: -2174.435426
EM: Round [268] log likelihood: -2174.434302
EM: Round [269] log likelihood: -2174.433187
EM: Round [270] log likelihood: -2174.432081
EM: Round [271] log likelihood: -2174.430982
EM: Round [272] log likelihood: -2174.429893
EM: Round [273] log likelihood: -2174.428812
EM: Round [274] log likelihood: -2174.427739
EM: Round [275] log likelihood: -2174.426674
EM: Round [276] log likelihood: -2174.425618
EM: Round [277] log likelihood: -2174.424569
EM: Round [278] log likelihood: -2174.423529
EM: Round [279] log likelihood: -2174.422497
EM: Round [280] log likelihood: -2174.421472
EM: Round [281] log likelihood: -2174.420456
EM: Round [282] log likelihood: -2174.419447
EM: Round [283] log likelihood: -2174.418446
EM: Round [284] log likelihood: -2174.417453
EM: Round [285] log likelihood: -2174.416467
EM: Round [286] log likelihood: -2174.415489
EM: Round [287] log likelihood: -2174.414518
EM: Round [288] log likelihood: -2174.413555
EM: Round [289] log likelihood: -2174.412599
EM: Round [290] log likelihood: -2174.411651
EM: Round [291] log likelihood: -2174.410709
EM: Round [292] log likelihood: -2174.409775
EM: Round [293] log likelihood: -2174.408848
EM: Round [294] log likelihood: -2174.407928
EM: Round [295] log likelihood: -2174.407015
EM: Round [296] log likelihood: -2174.406109
EM: Round [297] log likelihood: -2174.405210
EM: Round [298] log likelihood: -2174.404318
EM: Round [299] log likelihood: -2174.403433
EM: Round [300] log likelihood: -2174.402554
EM: Round [301] log likelihood: -2174.401682
EM: Round [302] log likelihood: -2174.400817
EM: Round [303] log likelihood: -2174.399958
EM: Round [304] log likelihood: -2174.399106
EM: Round [305] log likelihood: -2174.398260
EM: Round [306] log likelihood: -2174.397420
EM: Round [307] log likelihood: -2174.396587
EM: Round [308] log likelihood: -2174.395760
EM: Round [309] log likelihood: -2174.394940
EM: Round [310] log likelihood: -2174.394126
EM: Round [311] log likelihood: -2174.393318
EM: Round [312] log likelihood: -2174.392516
EM: Round [313] log likelihood: -2174.391720
EM: Round [314] log likelihood: -2174.390930
EM: Round [315] log likelihood: -2174.390146
EM: Round [316] log likelihood: -2174.389368
EM: Round [317] log likelihood: -2174.388596
EM: Round [318] log likelihood: -2174.387830
EM: Round [319] log likelihood: -2174.387069
EM: Round [320] log likelihood: -2174.386314
EM: Round [321] log likelihood: -2174.385565
EM: Round [322] log likelihood: -2174.384822
EM: Round [323] log likelihood: -2174.384084
EM: Round [324] log likelihood: -2174.383352
EM: Round [325] log likelihood: -2174.382625
EM: Round [326] log likelihood: -2174.381904
EM: Round [327] log likelihood: -2174.381188
EM: Round [328] log likelihood: -2174.380477
EM: Round [329] log likelihood: -2174.379772
EM: Round [330] log likelihood: -2174.379072
EM: Round [331] log likelihood: -2174.378378
EM: Round [332] log likelihood: -2174.377689
EM: Round [333] log likelihood: -2174.377004
EM: Round [334] log likelihood: -2174.376325
EM: Round [335] log likelihood: -2174.375651
EM: Round [336] log likelihood: -2174.374983
EM: Round [337] log likelihood: -2174.374319
EM: Round [338] log likelihood: -2174.373660
EM: Round [339] log likelihood: -2174.373006
EM: Round [340] log likelihood: -2174.372357
EM: Round [341] log likelihood: -2174.371713
EM: Round [342] log likelihood: -2174.371073
EM: Round [343] log likelihood: -2174.370439
EM: Round [344] log likelihood: -2174.369809
EM: Round [345] log likelihood: -2174.369184
EM: Round [346] log likelihood: -2174.368563
EM: Round [347] log likelihood: -2174.367947
EM: Round [348] log likelihood: -2174.367336
EM: Round [349] log likelihood: -2174.366730
EM: Round [350] log likelihood: -2174.366127
EM: Round [351] log likelihood: -2174.365530
EM: Round [352] log likelihood: -2174.364937
EM: Round [353] log likelihood: -2174.364348
EM: Round [354] log likelihood: -2174.363764
EM: Round [355] log likelihood: -2174.363184
EM: Round [356] log likelihood: -2174.362608
EM: Round [357] log likelihood: -2174.362037
EM: Round [358] log likelihood: -2174.361470
EM: Round [359] log likelihood: -2174.360907
EM: Round [360] log likelihood: -2174.360348
EM: Round [361] log likelihood: -2174.359793
EM: Round [362] log likelihood: -2174.359243
EM: Round [363] log likelihood: -2174.358697
EM: Round [364] log likelihood: -2174.358154
EM: Round [365] log likelihood: -2174.357616
EM: Round [366] log likelihood: -2174.357082
EM: Round [367] log likelihood: -2174.356552
EM: Round [368] log likelihood: -2174.356025
EM: Round [369] log likelihood: -2174.355503
EM: Round [370] log likelihood: -2174.354985
EM: Round [371] log likelihood: -2174.354470
EM: Round [372] log likelihood: -2174.353959
EM: Round [373] log likelihood: -2174.353452
EM: Round [374] log likelihood: -2174.352949
EM: Round [375] log likelihood: -2174.352449
EM: Round [376] log likelihood: -2174.351953
EM: Round [377] log likelihood: -2174.351461
EM: Round [378] log likelihood: -2174.350973
EM: Round [379] log likelihood: -2174.350488
EM: Round [380] log likelihood: -2174.350006
EM: Round [381] log likelihood: -2174.349529
EM: Round [382] log likelihood: -2174.349054
EM: Round [383] log likelihood: -2174.348584
EM: Round [384] log likelihood: -2174.348116
EM: Round [385] log likelihood: -2174.347653
EM: Round [386] log likelihood: -2174.347192
EM: Round [387] log likelihood: -2174.346735
EM: Round [388] log likelihood: -2174.346282
EM: Round [389] log likelihood: -2174.345832
EM: Round [390] log likelihood: -2174.345385
EM: Round [391] log likelihood: -2174.344941
EM: Round [392] log likelihood: -2174.344501
EM: Round [393] log likelihood: -2174.344064
EM: Round [394] log likelihood: -2174.343630
EM: Round [395] log likelihood: -2174.343200
EM: Round [396] log likelihood: -2174.342772
EM: Round [397] log likelihood: -2174.342348
EM: Round [398] log likelihood: -2174.341927
EM: Round [399] log likelihood: -2174.341509
EM: Round [400] log likelihood: -2174.341094
EM: Round [401] log likelihood: -2174.340682
EM: Round [402] log likelihood: -2174.340273
EM: Round [403] log likelihood: -2174.339867
EM: Round [404] log likelihood: -2174.339464
EM: Round [405] log likelihood: -2174.339064
EM: Round [406] log likelihood: -2174.338667
EM: Round [407] log likelihood: -2174.338273
EM: Round [408] log likelihood: -2174.337882
EM: Round [409] log likelihood: -2174.337494
EM: Round [410] log likelihood: -2174.337109
EM: Round [411] log likelihood: -2174.336726
EM: Round [412] log likelihood: -2174.336346
EM: Round [413] log likelihood: -2174.335969
EM: Round [414] log likelihood: -2174.335595
EM: Round [415] log likelihood: -2174.335224
EM: Round [416] log likelihood: -2174.334855
EM: Round [417] log likelihood: -2174.334489
EM: Round [418] log likelihood: -2174.334126
EM: Round [419] log likelihood: -2174.333765
EM: Round [420] log likelihood: -2174.333407
EM: Round [421] log likelihood: -2174.333052
EM: Round [422] log likelihood: -2174.332699
EM: Round [423] log likelihood: -2174.332349
EM: Round [424] log likelihood: -2174.332002
EM: Round [425] log likelihood: -2174.331657
EM: Round [426] log likelihood: -2174.331314
EM: Round [427] log likelihood: -2174.330974
EM: Round [428] log likelihood: -2174.330637
EM: Round [429] log likelihood: -2174.330302
EM: Round [430] log likelihood: -2174.329969
EM: Round [431] log likelihood: -2174.329639
EM: Round [432] log likelihood: -2174.329311
EM: Round [433] log likelihood: -2174.328986
EM: Round [434] log likelihood: -2174.328663
EM: Round [435] log likelihood: -2174.328343
EM: Round [436] log likelihood: -2174.328025
EM: Round [437] log likelihood: -2174.327709
EM: Round [438] log likelihood: -2174.327395
EM: Round [439] log likelihood: -2174.327084
EM: Round [440] log likelihood: -2174.326775
EM: Round [441] log likelihood: -2174.326468
EM: Round [442] log likelihood: -2174.326164
EM: Round [443] log likelihood: -2174.325862
EM: Round [444] log likelihood: -2174.325562
EM: Round [445] log likelihood: -2174.325264
EM: Round [446] log likelihood: -2174.324968
EM: Round [447] log likelihood: -2174.324675
EM: Round [448] log likelihood: -2174.324383
EM: Round [449] log likelihood: -2174.324094
EM: Round [450] log likelihood: -2174.323807
EM: Round [451] log likelihood: -2174.323522
EM: Round [452] log likelihood: -2174.323239
EM: Round [453] log likelihood: -2174.322958
EM: Round [454] log likelihood: -2174.322680
EM: Round [455] log likelihood: -2174.322403
EM: Round [456] log likelihood: -2174.322128
EM: Round [457] log likelihood: -2174.321855
EM: Round [458] log likelihood: -2174.321585
EM: Round [459] log likelihood: -2174.321316
EM: Round [460] log likelihood: -2174.321049
EM: Round [461] log likelihood: -2174.320784
EM: Round [462] log likelihood: -2174.320521
EM: Round [463] log likelihood: -2174.320260
EM: Round [464] log likelihood: -2174.320001
EM: Round [465] log likelihood: -2174.319744
EM: Round [466] log likelihood: -2174.319489
EM: Round [467] log likelihood: -2174.319235
EM: Round [468] log likelihood: -2174.318984
EM: Round [469] log likelihood: -2174.318734
EM: Round [470] log likelihood: -2174.318486
EM: Round [471] log likelihood: -2174.318240
EM: Round [472] log likelihood: -2174.317995
EM: Round [473] log likelihood: -2174.317753
EM: Round [474] log likelihood: -2174.317512
EM: Round [475] log likelihood: -2174.317273
EM: Round [476] log likelihood: -2174.317036
EM: Round [477] log likelihood: -2174.316800
EM: Round [478] log likelihood: -2174.316566
EM: Round [479] log likelihood: -2174.316334
EM: Round [480] log likelihood: -2174.316104
EM: Round [481] log likelihood: -2174.315875
EM: Round [482] log likelihood: -2174.315648
EM: Round [483] log likelihood: -2174.315422
EM: Round [484] log likelihood: -2174.315199
EM: Round [485] log likelihood: -2174.314976
EM: Round [486] log likelihood: -2174.314756
EM: Round [487] log likelihood: -2174.314537
EM: Round [488] log likelihood: -2174.314319
EM: Round [489] log likelihood: -2174.314104
EM: Round [490] log likelihood: -2174.313889
EM: Round [491] log likelihood: -2174.313677
EM: Round [492] log likelihood: -2174.313466
EM: Round [493] log likelihood: -2174.313256
EM: Round [494] log likelihood: -2174.313048
EM: Round [495] log likelihood: -2174.312841
EM: Round [496] log likelihood: -2174.312636
EM: Round [497] log likelihood: -2174.312433
EM: Round [498] log likelihood: -2174.312231
EM: Round [499] log likelihood: -2174.312030
EM: Round [500] log likelihood: -2174.311831
EM: Round [501] log likelihood: -2174.311633
EM: Round [502] log likelihood: -2174.311437
EM: Round [503] log likelihood: -2174.311242
EM: Round [504] log likelihood: -2174.311049
EM: Round [505] log likelihood: -2174.310857
EM: Round [506] log likelihood: -2174.310666
EM: Round [507] log likelihood: -2174.310477
EM: Round [508] log likelihood: -2174.310289
EM: Round [509] log likelihood: -2174.310103
EM: Round [510] log likelihood: -2174.309917
EM: Round [511] log likelihood: -2174.309734
EM: Round [512] log likelihood: -2174.309551
EM: Round [513] log likelihood: -2174.309370
EM: Round [514] log likelihood: -2174.309190
EM: Round [515] log likelihood: -2174.309012
EM: Round [516] log likelihood: -2174.308834
EM: Round [517] log likelihood: -2174.308658
EM: Round [518] log likelihood: -2174.308484
EM: Round [519] log likelihood: -2174.308310
EM: Round [520] log likelihood: -2174.308138
EM: Round [521] log likelihood: -2174.307967
EM: Round [522] log likelihood: -2174.307798
EM: Round [523] log likelihood: -2174.307629
EM: Round [524] log likelihood: -2174.307462
EM: Round [525] log likelihood: -2174.307296
EM: Round [526] log likelihood: -2174.307131
EM: Round [527] log likelihood: -2174.306968
EM: Round [528] log likelihood: -2174.306805
EM: Round [529] log likelihood: -2174.306644
EM: Round [530] log likelihood: -2174.306484
EM: Round [531] log likelihood: -2174.306325
EM: Round [532] log likelihood: -2174.306167
EM: Round [533] log likelihood: -2174.306011
EM: Round [534] log likelihood: -2174.305855
EM: Round [535] log likelihood: -2174.305701
EM: Round [536] log likelihood: -2174.305548
EM: Round [537] log likelihood: -2174.305396
EM: Round [538] log likelihood: -2174.305245
EM: Round [539] log likelihood: -2174.305095
EM: Round [540] log likelihood: -2174.304946
EM: Round [541] log likelihood: -2174.304798
EM: Round [542] log likelihood: -2174.304651
EM: Round [543] log likelihood: -2174.304506
EM: Round [544] log likelihood: -2174.304361
EM: Round [545] log likelihood: -2174.304218
EM: Round [546] log likelihood: -2174.304075
EM: Round [547] log likelihood: -2174.303934
EM: Round [548] log likelihood: -2174.303793
EM: Round [549] log likelihood: -2174.303654
EM: Round [550] log likelihood: -2174.303515
EM: Round [551] log likelihood: -2174.303378
EM: Round [552] log likelihood: -2174.303242
EM: Round [553] log likelihood: -2174.303106
EM: Round [554] log likelihood: -2174.302972
EM: Round [555] log likelihood: -2174.302838
EM: Round [556] log likelihood: -2174.302706
EM: Round [557] log likelihood: -2174.302574
EM: Round [558] log likelihood: -2174.302444
EM: Round [559] log likelihood: -2174.302314
EM: Round [560] log likelihood: -2174.302185
EM: Round [561] log likelihood: -2174.302058
EM: Round [562] log likelihood: -2174.301931
EM: Round [563] log likelihood: -2174.301805
EM: Round [564] log likelihood: -2174.301680
EM: Round [565] log likelihood: -2174.301556
EM: Round [566] log likelihood: -2174.301432
EM: Round [567] log likelihood: -2174.301310
EM: Round [568] log likelihood: -2174.301189
EM: Round [569] log likelihood: -2174.301068
EM: Round [570] log likelihood: -2174.300948
EM: Round [571] log likelihood: -2174.300830
EM: Round [572] log likelihood: -2174.300712
EM: Round [573] log likelihood: -2174.300594
EM: Round [574] log likelihood: -2174.300478
EM: Round [575] log likelihood: -2174.300363
EM: Round [576] log likelihood: -2174.300248
EM: Round [577] log likelihood: -2174.300134
EM: Round [578] log likelihood: -2174.300021
EM: Round [579] log likelihood: -2174.299909
EM: Round [580] log likelihood: -2174.299798
EM: Round [581] log likelihood: -2174.299687
EM: Round [582] log likelihood: -2174.299578
EM: Round [583] log likelihood: -2174.299469
EM: Round [584] log likelihood: -2174.299361
EM: Round [585] log likelihood: -2174.299253
EM: Round [586] log likelihood: -2174.299147
EM: Round [587] log likelihood: -2174.299041
EM: Round [588] log likelihood: -2174.298936
EM: Round [589] log likelihood: -2174.298831
EM: Round [590] log likelihood: -2174.298728
EM: Round [591] log likelihood: -2174.298625
EM: Round [592] log likelihood: -2174.298523
EM: Round [593] log likelihood: -2174.298422
EM: Round [594] log likelihood: -2174.298321
EM: Round [595] log likelihood: -2174.298221
EM: Stopping iterations at round 595 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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || :
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.Wyv1hwOhSd/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2062.152484
EM: Round [1] log likelihood: -2062.138401
EM: Round [2] log likelihood: -2062.124516
EM: Round [3] log likelihood: -2062.110826
EM: Round [4] log likelihood: -2062.097325
EM: Round [5] log likelihood: -2062.084011
EM: Round [6] log likelihood: -2062.070880
EM: Round [7] log likelihood: -2062.057927
EM: Round [8] log likelihood: -2062.045150
EM: Round [9] log likelihood: -2062.032545
EM: Round [10] log likelihood: -2062.020108
EM: Round [11] log likelihood: -2062.007836
EM: Round [12] log likelihood: -2061.995726
EM: Round [13] log likelihood: -2061.983775
EM: Round [14] log likelihood: -2061.971981
EM: Round [15] log likelihood: -2061.960339
EM: Round [16] log likelihood: -2061.948847
EM: Round [17] log likelihood: -2061.937502
EM: Round [18] log likelihood: -2061.926302
EM: Round [19] log likelihood: -2061.915244
EM: Round [20] log likelihood: -2061.904326
EM: Round [21] log likelihood: -2061.893544
EM: Round [22] log likelihood: -2061.882897
EM: Round [23] log likelihood: -2061.872382
EM: Round [24] log likelihood: -2061.861997
EM: Round [25] log likelihood: -2061.851739
EM: Round [26] log likelihood: -2061.841607
EM: Round [27] log likelihood: -2061.831598
EM: Round [28] log likelihood: -2061.821709
EM: Round [29] log likelihood: -2061.811940
EM: Round [30] log likelihood: -2061.802288
EM: Round [31] log likelihood: -2061.792751
EM: Round [32] log likelihood: -2061.783327
EM: Round [33] log likelihood: -2061.774014
EM: Round [34] log likelihood: -2061.764811
EM: Round [35] log likelihood: -2061.755716
EM: Round [36] log likelihood: -2061.746726
EM: Round [37] log likelihood: -2061.737841
EM: Round [38] log likelihood: -2061.729058
EM: Round [39] log likelihood: -2061.720376
EM: Round [40] log likelihood: -2061.711794
EM: Round [41] log likelihood: -2061.703309
EM: Round [42] log likelihood: -2061.694920
EM: Round [43] log likelihood: -2061.686627
EM: Round [44] log likelihood: -2061.678427
EM: Round [45] log likelihood: -2061.670318
EM: Round [46] log likelihood: -2061.662300
EM: Round [47] log likelihood: -2061.654372
EM: Round [48] log likelihood: -2061.646531
EM: Round [49] log likelihood: -2061.638776
EM: Round [50] log likelihood: -2061.631107
EM: Round [51] log likelihood: -2061.623522
EM: Round [52] log likelihood: -2061.616019
EM: Round [53] log likelihood: -2061.608598
EM: Round [54] log likelihood: -2061.601258
EM: Round [55] log likelihood: -2061.593996
EM: Round [56] log likelihood: -2061.586813
EM: Round [57] log likelihood: -2061.579706
EM: Round [58] log likelihood: -2061.572676
EM: Round [59] log likelihood: -2061.565720
EM: Round [60] log likelihood: -2061.558838
EM: Round [61] log likelihood: -2061.552028
EM: Round [62] log likelihood: -2061.545290
EM: Round [63] log likelihood: -2061.538623
EM: Round [64] log likelihood: -2061.532026
EM: Round [65] log likelihood: -2061.525497
EM: Round [66] log likelihood: -2061.519036
EM: Round [67] log likelihood: -2061.512642
EM: Round [68] log likelihood: -2061.506314
EM: Round [69] log likelihood: -2061.500051
EM: Round [70] log likelihood: -2061.493853
EM: Round [71] log likelihood: -2061.487718
EM: Round [72] log likelihood: -2061.481645
EM: Round [73] log likelihood: -2061.475634
EM: Round [74] log likelihood: -2061.469684
EM: Round [75] log likelihood: -2061.463794
EM: Round [76] log likelihood: -2061.457963
EM: Round [77] log likelihood: -2061.452191
EM: Round [78] log likelihood: -2061.446477
EM: Round [79] log likelihood: -2061.440820
EM: Round [80] log likelihood: -2061.435219
EM: Round [81] log likelihood: -2061.429674
EM: Round [82] log likelihood: -2061.424183
EM: Round [83] log likelihood: -2061.418747
EM: Round [84] log likelihood: -2061.413365
EM: Round [85] log likelihood: -2061.408035
EM: Round [86] log likelihood: -2061.402757
EM: Round [87] log likelihood: -2061.397532
EM: Round [88] log likelihood: -2061.392357
EM: Round [89] log likelihood: -2061.387232
EM: Round [90] log likelihood: -2061.382157
EM: Round [91] log likelihood: -2061.377131
EM: Round [92] log likelihood: -2061.372154
EM: Round [93] log likelihood: -2061.367224
EM: Round [94] log likelihood: -2061.362342
EM: Round [95] log likelihood: -2061.357507
EM: Round [96] log likelihood: -2061.352718
EM: Round [97] log likelihood: -2061.347974
EM: Round [98] log likelihood: -2061.343276
EM: Round [99] log likelihood: -2061.338622
EM: Round [100] log likelihood: -2061.334012
EM: Round [101] log likelihood: -2061.329446
EM: Round [102] log likelihood: -2061.324923
EM: Round [103] log likelihood: -2061.320442
EM: Round [104] log likelihood: -2061.316003
EM: Round [105] log likelihood: -2061.311606
EM: Round [106] log likelihood: -2061.307250
EM: Round [107] log likelihood: -2061.302934
EM: Round [108] log likelihood: -2061.298659
EM: Round [109] log likelihood: -2061.294423
EM: Round [110] log likelihood: -2061.290227
EM: Round [111] log likelihood: -2061.286069
EM: Round [112] log likelihood: -2061.281950
EM: Round [113] log likelihood: -2061.277868
EM: Round [114] log likelihood: -2061.273824
EM: Round [115] log likelihood: -2061.269818
EM: Round [116] log likelihood: -2061.265847
EM: Round [117] log likelihood: -2061.261913
EM: Round [118] log likelihood: -2061.258015
EM: Round [119] log likelihood: -2061.254152
EM: Round [120] log likelihood: -2061.250325
EM: Round [121] log likelihood: -2061.246532
EM: Round [122] log likelihood: -2061.242773
EM: Round [123] log likelihood: -2061.239048
EM: Round [124] log likelihood: -2061.235357
EM: Round [125] log likelihood: -2061.231699
EM: Round [126] log likelihood: -2061.228074
EM: Round [127] log likelihood: -2061.224481
EM: Round [128] log likelihood: -2061.220920
EM: Round [129] log likelihood: -2061.217391
EM: Round [130] log likelihood: -2061.213894
EM: Round [131] log likelihood: -2061.210428
EM: Round [132] log likelihood: -2061.206992
EM: Round [133] log likelihood: -2061.203587
EM: Round [134] log likelihood: -2061.200212
EM: Round [135] log likelihood: -2061.196867
EM: Round [136] log likelihood: -2061.193552
EM: Round [137] log likelihood: -2061.190265
EM: Round [138] log likelihood: -2061.187008
EM: Round [139] log likelihood: -2061.183779
EM: Round [140] log likelihood: -2061.180578
EM: Round [141] log likelihood: -2061.177406
EM: Round [142] log likelihood: -2061.174261
EM: Round [143] log likelihood: -2061.171143
EM: Round [144] log likelihood: -2061.168053
EM: Round [145] log likelihood: -2061.164989
EM: Round [146] log likelihood: -2061.161953
EM: Round [147] log likelihood: -2061.158942
EM: Round [148] log likelihood: -2061.155957
EM: Round [149] log likelihood: -2061.152999
EM: Round [150] log likelihood: -2061.150066
EM: Round [151] log likelihood: -2061.147158
EM: Round [152] log likelihood: -2061.144275
EM: Round [153] log likelihood: -2061.141417
EM: Round [154] log likelihood: -2061.138583
EM: Round [155] log likelihood: -2061.135774
EM: Round [156] log likelihood: -2061.132989
EM: Round [157] log likelihood: -2061.130227
EM: Round [158] log likelihood: -2061.127489
EM: Round [159] log likelihood: -2061.124775
EM: Round [160] log likelihood: -2061.122083
EM: Round [161] log likelihood: -2061.119415
EM: Round [162] log likelihood: -2061.116769
EM: Round [163] log likelihood: -2061.114145
EM: Round [164] log likelihood: -2061.111544
EM: Round [165] log likelihood: -2061.108965
EM: Round [166] log likelihood: -2061.106407
EM: Round [167] log likelihood: -2061.103871
EM: Round [168] log likelihood: -2061.101357
EM: Round [169] log likelihood: -2061.098863
EM: Round [170] log likelihood: -2061.096391
EM: Round [171] log likelihood: -2061.093939
EM: Round [172] log likelihood: -2061.091508
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EM: Round [534] log likelihood: -2060.801892
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EM: Round [542] log likelihood: -2060.800688
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EM: Round [564] log likelihood: -2060.797717
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EM: Round [567] log likelihood: -2060.797347
EM: Round [568] log likelihood: -2060.797225
EM: Round [569] log likelihood: -2060.797105
EM: Round [570] log likelihood: -2060.796985
EM: Round [571] log likelihood: -2060.796866
EM: Round [572] log likelihood: -2060.796748
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EM: Round [576] log likelihood: -2060.796285
EM: Round [577] log likelihood: -2060.796171
EM: Round [578] log likelihood: -2060.796058
EM: Round [579] log likelihood: -2060.795946
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EM: Round [581] log likelihood: -2060.795724
EM: Round [582] log likelihood: -2060.795615
EM: Round [583] log likelihood: -2060.795506
EM: Round [584] log likelihood: -2060.795397
EM: Round [585] log likelihood: -2060.795290
EM: Round [586] log likelihood: -2060.795183
EM: Round [587] log likelihood: -2060.795078
EM: Round [588] log likelihood: -2060.794973
EM: Round [589] log likelihood: -2060.794868
EM: Round [590] log likelihood: -2060.794765
EM: Round [591] log likelihood: -2060.794662
EM: Round [592] log likelihood: -2060.794560
EM: Round [593] log likelihood: -2060.794459
EM: Round [594] log likelihood: -2060.794358
EM: Round [595] log likelihood: -2060.794258
EM: Stopping iterations at round 595 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.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 281966738
Execution Time = 4.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Wyv1hwOhSd/fi_workdir/microH.dat
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Wyv1hwOhSd/fi_workdir/microH.dat /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Wyv1hwOhSd/fi_workdir/microH.dat /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Wyv1hwOhSd --json_outfile /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Wyv1hwOhSd --json_outfile /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.Wyv1hwOhSd/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.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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 [ENSG00000273252.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Wyv1hwOhSd/ctat_genome_lib_build_dir > /tmp/nxf.Wyv1hwOhSd/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.Wyv1hwOhSd/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory