Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/fd6282bf2e6b55224bfa4a48e0e0f6/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/fd6282bf2e6b55224bfa4a48e0e0f6/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/a9f5ad55397a66e7f6d23213865a14/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/a9f5ad55397a66e7f6d23213865a14/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/02d95b24f6df1a0ceeb676c6f7951b/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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 aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5gGev74vOT/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5gGev74vOT/cytoBand.txt
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.5gGev74vOT/fi_workdir --reads "/tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.5gGev74vOT/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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:00:31 ..... started STAR run
Jun 08 10:00:31 ..... loading genome
Jun 08 10:02:12 ... generating Suffix Array index
Jun 08 10:05:52 ... completed Suffix Array index
Jun 08 10:05:52 ..... processing annotations GTF
Jun 08 10:05:52 ..... inserting junctions into the genome indices
Jun 08 10:06:53 ..... started mapping
Jun 08 11:01:34 ..... finished mapping
Jun 08 11:01:36 ..... started sorting BAM
Jun 08 11:01:36 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 61.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.5gGev74vOT/fi_workdir --reads "/tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:01:44 : INFO : Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   
[160000]   
[170000]   
[180000]   
[190000]   
[200000]   
[210000]   
[220000]   
[230000]   
[240000]   
[250000]   
[260000]   
[270000]   
[280000]   
[290000]   
[300000]   
[310000]   
[320000]   
[330000]   
[340000]   
[350000]   
[360000]   
[370000]   
[380000]   
[390000]   
[400000]   
[410000]   
[420000]   
[430000]   
[440000]   
[450000]   
[460000]   
[470000]   
[480000]   
[490000]   
[500000]   
[510000]   
[520000]   
[530000]   
[540000]   
[550000]   
[560000]   
[570000]   
[580000]   
[590000]   
[600000]   
[610000]   
[620000]   
[630000]   
[640000]   
[650000]   
[660000]   
[670000]   
[680000]   
[690000]   
[700000]   
[710000]   
[720000]   
[730000]   
[740000]   
[750000]   
[760000]   
[770000]   
[780000]   
[790000]   
[800000]   
[810000]   
[820000]   
[830000]   
[840000]   
[850000]   
[860000]   
[870000]   
[880000]   
[890000]   
[900000]   
[910000]   
[920000]   
[930000]   
[940000]   
[950000]   
[960000]   
[970000]   
[980000]   
[990000]   
[1000000]   
[1010000]   
[1020000]   
[1030000]   
[1040000]   
[1050000]   
[1060000]   
[1070000]   
[1080000]   
[1090000]   
[1100000]   
[1110000]   
[1120000]   
[1130000]   
[1140000]   
[1150000]   
[1160000]   
[1170000]   
[1180000]   
[1190000]   
[1200000]   
[1210000]   
[1220000]   
[1230000]   
[1240000]   
[1250000]   
[1260000]   
[1270000]   
[1280000]   
[1290000]   
[1300000]   
[1310000]   
[1320000]   -done parsing /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
          'small anchor length' => 118,
          'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
          'per_id < 96' => 3765,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 12,
          'excessive soft clipping' => 4343,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
          ' ** passed ** ' => 15787,
          'seq-similar region overlap' => 181,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 28,
          'low complexity anchor region' => 33,
          'num genes matched < 2' => 12,
          'exons hit < 2' => 12,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 63
        };
-writing fusion junction support info.
Execution Time = 0.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: INPP4A--DPP10

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: MRPS28--RN7SL323P

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: MRPS28--AC046176.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TTC8--AL135746.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2950,
          'seq similar region alignment' => 53524
        };
Execution Time = 1.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4628.914988
EM: Round [1] log likelihood: -4627.706253
EM: Round [2] log likelihood: -4626.918580
EM: Round [3] log likelihood: -4626.268723
EM: Round [4] log likelihood: -4625.727668
EM: Round [5] log likelihood: -4625.273462
EM: Round [6] log likelihood: -4624.889039
EM: Round [7] log likelihood: -4624.561017
EM: Round [8] log likelihood: -4624.278837
EM: Round [9] log likelihood: -4624.034119
EM: Round [10] log likelihood: -4623.820177
EM: Round [11] log likelihood: -4623.631651
EM: Round [12] log likelihood: -4623.464226
EM: Round [13] log likelihood: -4623.314415
EM: Round [14] log likelihood: -4623.179387
EM: Round [15] log likelihood: -4623.056834
EM: Round [16] log likelihood: -4622.944869
EM: Round [17] log likelihood: -4622.841943
EM: Round [18] log likelihood: -4622.746777
EM: Round [19] log likelihood: -4622.658313
EM: Round [20] log likelihood: -4622.575669
EM: Round [21] log likelihood: -4622.498110
EM: Round [22] log likelihood: -4622.425021
EM: Round [23] log likelihood: -4622.355882
EM: Round [24] log likelihood: -4622.290253
EM: Round [25] log likelihood: -4622.227761
EM: Round [26] log likelihood: -4622.168087
EM: Round [27] log likelihood: -4622.110959
EM: Round [28] log likelihood: -4622.056140
EM: Round [29] log likelihood: -4622.003429
EM: Round [30] log likelihood: -4621.952648
EM: Round [31] log likelihood: -4621.903643
EM: Round [32] log likelihood: -4621.856279
EM: Round [33] log likelihood: -4621.810438
EM: Round [34] log likelihood: -4621.766016
EM: Round [35] log likelihood: -4621.722918
EM: Round [36] log likelihood: -4621.681062
EM: Round [37] log likelihood: -4621.640375
EM: Round [38] log likelihood: -4621.600790
EM: Round [39] log likelihood: -4621.562248
EM: Round [40] log likelihood: -4621.524694
EM: Round [41] log likelihood: -4621.488079
EM: Round [42] log likelihood: -4621.452360
EM: Round [43] log likelihood: -4621.417494
EM: Round [44] log likelihood: -4621.383444
EM: Round [45] log likelihood: -4621.350177
EM: Round [46] log likelihood: -4621.317659
EM: Round [47] log likelihood: -4621.285862
EM: Round [48] log likelihood: -4621.254758
EM: Round [49] log likelihood: -4621.224321
EM: Round [50] log likelihood: -4621.194528
EM: Round [51] log likelihood: -4621.165356
EM: Round [52] log likelihood: -4621.136783
EM: Round [53] log likelihood: -4621.108791
EM: Round [54] log likelihood: -4621.081359
EM: Round [55] log likelihood: -4621.054470
EM: Round [56] log likelihood: -4621.028107
EM: Round [57] log likelihood: -4621.002254
EM: Round [58] log likelihood: -4620.976896
EM: Round [59] log likelihood: -4620.952017
EM: Round [60] log likelihood: -4620.927604
EM: Round [61] log likelihood: -4620.903643
EM: Round [62] log likelihood: -4620.880121
EM: Round [63] log likelihood: -4620.857026
EM: Round [64] log likelihood: -4620.834346
EM: Round [65] log likelihood: -4620.812069
EM: Round [66] log likelihood: -4620.790184
EM: Round [67] log likelihood: -4620.768681
EM: Round [68] log likelihood: -4620.747550
EM: Round [69] log likelihood: -4620.726780
EM: Round [70] log likelihood: -4620.706361
EM: Round [71] log likelihood: -4620.686285
EM: Round [72] log likelihood: -4620.666543
EM: Round [73] log likelihood: -4620.647125
EM: Round [74] log likelihood: -4620.628024
EM: Round [75] log likelihood: -4620.609231
EM: Round [76] log likelihood: -4620.590739
EM: Round [77] log likelihood: -4620.572539
EM: Round [78] log likelihood: -4620.554625
EM: Round [79] log likelihood: -4620.536989
EM: Round [80] log likelihood: -4620.519625
EM: Round [81] log likelihood: -4620.502525
EM: Round [82] log likelihood: -4620.485683
EM: Round [83] log likelihood: -4620.469093
EM: Round [84] log likelihood: -4620.452749
EM: Round [85] log likelihood: -4620.436645
EM: Round [86] log likelihood: -4620.420774
EM: Round [87] log likelihood: -4620.405132
EM: Round [88] log likelihood: -4620.389713
EM: Round [89] log likelihood: -4620.374512
EM: Round [90] log likelihood: -4620.359523
EM: Round [91] log likelihood: -4620.344742
EM: Round [92] log likelihood: -4620.330164
EM: Round [93] log likelihood: -4620.315785
EM: Round [94] log likelihood: -4620.301599
EM: Round [95] log likelihood: -4620.287602
EM: Round [96] log likelihood: -4620.273791
EM: Round [97] log likelihood: -4620.260161
EM: Round [98] log likelihood: -4620.246708
EM: Round [99] log likelihood: -4620.233428
EM: Round [100] log likelihood: -4620.220317
EM: Round [101] log likelihood: -4620.207372
EM: Round [102] log likelihood: -4620.194589
EM: Round [103] log likelihood: -4620.181966
EM: Round [104] log likelihood: -4620.169497
EM: Round [105] log likelihood: -4620.157181
EM: Round [106] log likelihood: -4620.145014
EM: Round [107] log likelihood: -4620.132992
EM: Round [108] log likelihood: -4620.121114
EM: Round [109] log likelihood: -4620.109376
EM: Round [110] log likelihood: -4620.097775
EM: Round [111] log likelihood: -4620.086309
EM: Round [112] log likelihood: -4620.074975
EM: Round [113] log likelihood: -4620.063770
EM: Round [114] log likelihood: -4620.052692
EM: Round [115] log likelihood: -4620.041739
EM: Round [116] log likelihood: -4620.030907
EM: Round [117] log likelihood: -4620.020196
EM: Round [118] log likelihood: -4620.009602
EM: Round [119] log likelihood: -4619.999123
EM: Round [120] log likelihood: -4619.988758
EM: Round [121] log likelihood: -4619.978504
EM: Round [122] log likelihood: -4619.968360
EM: Round [123] log likelihood: -4619.958322
EM: Round [124] log likelihood: -4619.948390
EM: Round [125] log likelihood: -4619.938562
EM: Round [126] log likelihood: -4619.928835
EM: Round [127] log likelihood: -4619.919209
EM: Round [128] log likelihood: -4619.909681
EM: Round [129] log likelihood: -4619.900249
EM: Round [130] log likelihood: -4619.890913
EM: Round [131] log likelihood: -4619.881670
EM: Round [132] log likelihood: -4619.872519
EM: Round [133] log likelihood: -4619.863459
EM: Round [134] log likelihood: -4619.854487
EM: Round [135] log likelihood: -4619.845603
EM: Round [136] log likelihood: -4619.836806
EM: Round [137] log likelihood: -4619.828093
EM: Round [138] log likelihood: -4619.819464
EM: Round [139] log likelihood: -4619.810917
EM: Round [140] log likelihood: -4619.802452
EM: Round [141] log likelihood: -4619.794066
EM: Round [142] log likelihood: -4619.785759
EM: Round [143] log likelihood: -4619.777529
EM: Round [144] log likelihood: -4619.769375
EM: Round [145] log likelihood: -4619.761297
EM: Round [146] log likelihood: -4619.753293
EM: Round [147] log likelihood: -4619.745361
EM: Round [148] log likelihood: -4619.737502
EM: Round [149] log likelihood: -4619.729714
EM: Round [150] log likelihood: -4619.721996
EM: Round [151] log likelihood: -4619.714346
EM: Round [152] log likelihood: -4619.706765
EM: Round [153] log likelihood: -4619.699251
EM: Round [154] log likelihood: -4619.691803
EM: Round [155] log likelihood: -4619.684421
EM: Round [156] log likelihood: -4619.677103
EM: Round [157] log likelihood: -4619.669849
EM: Round [158] log likelihood: -4619.662657
EM: Round [159] log likelihood: -4619.655527
EM: Round [160] log likelihood: -4619.648459
EM: Round [161] log likelihood: -4619.641450
EM: Round [162] log likelihood: -4619.634502
EM: Round [163] log likelihood: -4619.627612
EM: Round [164] log likelihood: -4619.620780
EM: Round [165] log likelihood: -4619.614006
EM: Round [166] log likelihood: -4619.607289
EM: Round [167] log likelihood: -4619.600627
EM: Round [168] log likelihood: -4619.594020
EM: Round [169] log likelihood: -4619.587469
EM: Round [170] log likelihood: -4619.580971
EM: Round [171] log likelihood: -4619.574526
EM: Round [172] log likelihood: -4619.568134
EM: Round [173] log likelihood: -4619.561794
EM: Round [174] log likelihood: -4619.555506
EM: Round [175] log likelihood: -4619.549268
EM: Round [176] log likelihood: -4619.543081
EM: Round [177] log likelihood: -4619.536943
EM: Round [178] log likelihood: -4619.530854
EM: Round [179] log likelihood: -4619.524814
EM: Round [180] log likelihood: -4619.518821
EM: Round [181] log likelihood: -4619.512876
EM: Round [182] log likelihood: -4619.506978
EM: Round [183] log likelihood: -4619.501127
EM: Round [184] log likelihood: -4619.495321
EM: Round [185] log likelihood: -4619.489561
EM: Round [186] log likelihood: -4619.483845
EM: Round [187] log likelihood: -4619.478174
EM: Round [188] log likelihood: -4619.472546
EM: Round [189] log likelihood: -4619.466962
EM: Round [190] log likelihood: -4619.461421
EM: Round [191] log likelihood: -4619.455922
EM: Round [192] log likelihood: -4619.450466
EM: Round [193] log likelihood: -4619.445051
EM: Round [194] log likelihood: -4619.439677
EM: Round [195] log likelihood: -4619.434344
EM: Round [196] log likelihood: -4619.429051
EM: Round [197] log likelihood: -4619.423798
EM: Round [198] log likelihood: -4619.418584
EM: Round [199] log likelihood: -4619.413409
EM: Round [200] log likelihood: -4619.408273
EM: Round [201] log likelihood: -4619.403176
EM: Round [202] log likelihood: -4619.398116
EM: Round [203] log likelihood: -4619.393094
EM: Round [204] log likelihood: -4619.388108
EM: Round [205] log likelihood: -4619.383160
EM: Round [206] log likelihood: -4619.378248
EM: Round [207] log likelihood: -4619.373371
EM: Round [208] log likelihood: -4619.368531
EM: Round [209] log likelihood: -4619.363726
EM: Round [210] log likelihood: -4619.358955
EM: Round [211] log likelihood: -4619.354220
EM: Round [212] log likelihood: -4619.349518
EM: Round [213] log likelihood: -4619.344851
EM: Round [214] log likelihood: -4619.340217
EM: Round [215] log likelihood: -4619.335616
EM: Round [216] log likelihood: -4619.331049
EM: Round [217] log likelihood: -4619.326514
EM: Round [218] log likelihood: -4619.322011
EM: Round [219] log likelihood: -4619.317541
EM: Round [220] log likelihood: -4619.313102
EM: Round [221] log likelihood: -4619.308694
EM: Round [222] log likelihood: -4619.304318
EM: Round [223] log likelihood: -4619.299973
EM: Round [224] log likelihood: -4619.295658
EM: Round [225] log likelihood: -4619.291374
EM: Round [226] log likelihood: -4619.287119
EM: Round [227] log likelihood: -4619.282894
EM: Round [228] log likelihood: -4619.278699
EM: Round [229] log likelihood: -4619.274533
EM: Round [230] log likelihood: -4619.270396
EM: Round [231] log likelihood: -4619.266287
EM: Round [232] log likelihood: -4619.262207
EM: Round [233] log likelihood: -4619.258155
EM: Round [234] log likelihood: -4619.254131
EM: Round [235] log likelihood: -4619.250135
EM: Round [236] log likelihood: -4619.246166
EM: Round [237] log likelihood: -4619.242224
EM: Round [238] log likelihood: -4619.238310
EM: Round [239] log likelihood: -4619.234421
EM: Round [240] log likelihood: -4619.230560
EM: Round [241] log likelihood: -4619.226724
EM: Round [242] log likelihood: -4619.222915
EM: Round [243] log likelihood: -4619.219131
EM: Round [244] log likelihood: -4619.215373
EM: Round [245] log likelihood: -4619.211640
EM: Round [246] log likelihood: -4619.207932
EM: Round [247] log likelihood: -4619.204249
EM: Round [248] log likelihood: -4619.200591
EM: Round [249] log likelihood: -4619.196958
EM: Round [250] log likelihood: -4619.193348
EM: Round [251] log likelihood: -4619.189763
EM: Round [252] log likelihood: -4619.186201
EM: Round [253] log likelihood: -4619.182663
EM: Round [254] log likelihood: -4619.179149
EM: Round [255] log likelihood: -4619.175658
EM: Round [256] log likelihood: -4619.172190
EM: Round [257] log likelihood: -4619.168744
EM: Round [258] log likelihood: -4619.165322
EM: Round [259] log likelihood: -4619.161922
EM: Round [260] log likelihood: -4619.158544
EM: Round [261] log likelihood: -4619.155188
EM: Round [262] log likelihood: -4619.151854
EM: Round [263] log likelihood: -4619.148542
EM: Round [264] log likelihood: -4619.145252
EM: Round [265] log likelihood: -4619.141983
EM: Round [266] log likelihood: -4619.138735
EM: Round [267] log likelihood: -4619.135508
EM: Round [268] log likelihood: -4619.132302
EM: Round [269] log likelihood: -4619.129117
EM: Round [270] log likelihood: -4619.125953
EM: Round [271] log likelihood: -4619.122808
EM: Round [272] log likelihood: -4619.119684
EM: Round [273] log likelihood: -4619.116581
EM: Round [274] log likelihood: -4619.113496
EM: Round [275] log likelihood: -4619.110432
EM: Round [276] log likelihood: -4619.107387
EM: Round [277] log likelihood: -4619.104362
EM: Round [278] log likelihood: -4619.101356
EM: Round [279] log likelihood: -4619.098369
EM: Round [280] log likelihood: -4619.095401
EM: Round [281] log likelihood: -4619.092452
EM: Round [282] log likelihood: -4619.089522
EM: Round [283] log likelihood: -4619.086610
EM: Round [284] log likelihood: -4619.083717
EM: Round [285] log likelihood: -4619.080841
EM: Round [286] log likelihood: -4619.077984
EM: Round [287] log likelihood: -4619.075145
EM: Round [288] log likelihood: -4619.072324
EM: Round [289] log likelihood: -4619.069520
EM: Round [290] log likelihood: -4619.066734
EM: Round [291] log likelihood: -4619.063965
EM: Round [292] log likelihood: -4619.061214
EM: Round [293] log likelihood: -4619.058480
EM: Round [294] log likelihood: -4619.055763
EM: Round [295] log likelihood: -4619.053062
EM: Round [296] log likelihood: -4619.050379
EM: Round [297] log likelihood: -4619.047712
EM: Round [298] log likelihood: -4619.045062
EM: Round [299] log likelihood: -4619.042428
EM: Round [300] log likelihood: -4619.039810
EM: Round [301] log likelihood: -4619.037208
EM: Round [302] log likelihood: -4619.034623
EM: Round [303] log likelihood: -4619.032053
EM: Round [304] log likelihood: -4619.029499
EM: Round [305] log likelihood: -4619.026961
EM: Round [306] log likelihood: -4619.024439
EM: Round [307] log likelihood: -4619.021931
EM: Round [308] log likelihood: -4619.019440
EM: Round [309] log likelihood: -4619.016963
EM: Round [310] log likelihood: -4619.014502
EM: Round [311] log likelihood: -4619.012055
EM: Round [312] log likelihood: -4619.009623
EM: Round [313] log likelihood: -4619.007207
EM: Round [314] log likelihood: -4619.004804
EM: Round [315] log likelihood: -4619.002417
EM: Round [316] log likelihood: -4619.000044
EM: Round [317] log likelihood: -4618.997685
EM: Round [318] log likelihood: -4618.995340
EM: Round [319] log likelihood: -4618.993010
EM: Round [320] log likelihood: -4618.990693
EM: Round [321] log likelihood: -4618.988391
EM: Round [322] log likelihood: -4618.986102
EM: Round [323] log likelihood: -4618.983827
EM: Round [324] log likelihood: -4618.981566
EM: Round [325] log likelihood: -4618.979319
EM: Round [326] log likelihood: -4618.977084
EM: Round [327] log likelihood: -4618.974864
EM: Round [328] log likelihood: -4618.972656
EM: Round [329] log likelihood: -4618.970462
EM: Round [330] log likelihood: -4618.968280
EM: Round [331] log likelihood: -4618.966112
EM: Round [332] log likelihood: -4618.963956
EM: Round [333] log likelihood: -4618.961814
EM: Round [334] log likelihood: -4618.959684
EM: Round [335] log likelihood: -4618.957566
EM: Round [336] log likelihood: -4618.955462
EM: Round [337] log likelihood: -4618.953369
EM: Round [338] log likelihood: -4618.951289
EM: Round [339] log likelihood: -4618.949222
EM: Round [340] log likelihood: -4618.947166
EM: Round [341] log likelihood: -4618.945123
EM: Round [342] log likelihood: -4618.943091
EM: Round [343] log likelihood: -4618.941072
EM: Round [344] log likelihood: -4618.939064
EM: Round [345] log likelihood: -4618.937068
EM: Round [346] log likelihood: -4618.935084
EM: Round [347] log likelihood: -4618.933112
EM: Round [348] log likelihood: -4618.931151
EM: Round [349] log likelihood: -4618.929201
EM: Round [350] log likelihood: -4618.927263
EM: Round [351] log likelihood: -4618.925336
EM: Round [352] log likelihood: -4618.923421
EM: Round [353] log likelihood: -4618.921516
EM: Round [354] log likelihood: -4618.919623
EM: Round [355] log likelihood: -4618.917740
EM: Round [356] log likelihood: -4618.915869
EM: Round [357] log likelihood: -4618.914008
EM: Round [358] log likelihood: -4618.912158
EM: Round [359] log likelihood: -4618.910319
EM: Round [360] log likelihood: -4618.908491
EM: Round [361] log likelihood: -4618.906673
EM: Round [362] log likelihood: -4618.904865
EM: Round [363] log likelihood: -4618.903068
EM: Round [364] log likelihood: -4618.901282
EM: Round [365] log likelihood: -4618.899505
EM: Round [366] log likelihood: -4618.897739
EM: Round [367] log likelihood: -4618.895983
EM: Round [368] log likelihood: -4618.894237
EM: Round [369] log likelihood: -4618.892501
EM: Round [370] log likelihood: -4618.890775
EM: Round [371] log likelihood: -4618.889059
EM: Round [372] log likelihood: -4618.887353
EM: Round [373] log likelihood: -4618.885656
EM: Round [374] log likelihood: -4618.883969
EM: Round [375] log likelihood: -4618.882292
EM: Round [376] log likelihood: -4618.880624
EM: Round [377] log likelihood: -4618.878966
EM: Round [378] log likelihood: -4618.877317
EM: Round [379] log likelihood: -4618.875678
EM: Round [380] log likelihood: -4618.874048
EM: Round [381] log likelihood: -4618.872427
EM: Round [382] log likelihood: -4618.870816
EM: Round [383] log likelihood: -4618.869213
EM: Round [384] log likelihood: -4618.867620
EM: Round [385] log likelihood: -4618.866035
EM: Round [386] log likelihood: -4618.864460
EM: Round [387] log likelihood: -4618.862893
EM: Round [388] log likelihood: -4618.861336
EM: Round [389] log likelihood: -4618.859787
EM: Round [390] log likelihood: -4618.858247
EM: Round [391] log likelihood: -4618.856715
EM: Round [392] log likelihood: -4618.855192
EM: Round [393] log likelihood: -4618.853678
EM: Round [394] log likelihood: -4618.852172
EM: Round [395] log likelihood: -4618.850675
EM: Round [396] log likelihood: -4618.849186
EM: Round [397] log likelihood: -4618.847706
EM: Round [398] log likelihood: -4618.846233
EM: Round [399] log likelihood: -4618.844769
EM: Round [400] log likelihood: -4618.843313
EM: Round [401] log likelihood: -4618.841866
EM: Round [402] log likelihood: -4618.840426
EM: Round [403] log likelihood: -4618.838995
EM: Round [404] log likelihood: -4618.837571
EM: Round [405] log likelihood: -4618.836155
EM: Round [406] log likelihood: -4618.834748
EM: Round [407] log likelihood: -4618.833348
EM: Round [408] log likelihood: -4618.831955
EM: Round [409] log likelihood: -4618.830571
EM: Round [410] log likelihood: -4618.829194
EM: Round [411] log likelihood: -4618.827825
EM: Round [412] log likelihood: -4618.826464
EM: Round [413] log likelihood: -4618.825110
EM: Round [414] log likelihood: -4618.823763
EM: Round [415] log likelihood: -4618.822424
EM: Round [416] log likelihood: -4618.821093
EM: Round [417] log likelihood: -4618.819769
EM: Round [418] log likelihood: -4618.818452
EM: Round [419] log likelihood: -4618.817142
EM: Round [420] log likelihood: -4618.815840
EM: Round [421] log likelihood: -4618.814545
EM: Round [422] log likelihood: -4618.813256
EM: Round [423] log likelihood: -4618.811975
EM: Round [424] log likelihood: -4618.810702
EM: Round [425] log likelihood: -4618.809435
EM: Round [426] log likelihood: -4618.808175
EM: Round [427] log likelihood: -4618.806922
EM: Round [428] log likelihood: -4618.805675
EM: Round [429] log likelihood: -4618.804436
EM: Round [430] log likelihood: -4618.803204
EM: Round [431] log likelihood: -4618.801978
EM: Round [432] log likelihood: -4618.800759
EM: Round [433] log likelihood: -4618.799546
EM: Round [434] log likelihood: -4618.798340
EM: Round [435] log likelihood: -4618.797141
EM: Round [436] log likelihood: -4618.795949
EM: Round [437] log likelihood: -4618.794763
EM: Round [438] log likelihood: -4618.793583
EM: Round [439] log likelihood: -4618.792410
EM: Round [440] log likelihood: -4618.791243
EM: Round [441] log likelihood: -4618.790082
EM: Round [442] log likelihood: -4618.788928
EM: Round [443] log likelihood: -4618.787780
EM: Round [444] log likelihood: -4618.786639
EM: Round [445] log likelihood: -4618.785503
EM: Round [446] log likelihood: -4618.784374
EM: Round [447] log likelihood: -4618.783251
EM: Round [448] log likelihood: -4618.782134
EM: Round [449] log likelihood: -4618.781023
EM: Round [450] log likelihood: -4618.779918
EM: Round [451] log likelihood: -4618.778819
EM: Round [452] log likelihood: -4618.777726
EM: Round [453] log likelihood: -4618.776639
EM: Round [454] log likelihood: -4618.775558
EM: Round [455] log likelihood: -4618.774482
EM: Round [456] log likelihood: -4618.773413
EM: Round [457] log likelihood: -4618.772349
EM: Round [458] log likelihood: -4618.771291
EM: Round [459] log likelihood: -4618.770238
EM: Round [460] log likelihood: -4618.769192
EM: Round [461] log likelihood: -4618.768150
EM: Round [462] log likelihood: -4618.767115
EM: Round [463] log likelihood: -4618.766085
EM: Round [464] log likelihood: -4618.765061
EM: Round [465] log likelihood: -4618.764042
EM: Round [466] log likelihood: -4618.763029
EM: Round [467] log likelihood: -4618.762021
EM: Round [468] log likelihood: -4618.761018
EM: Round [469] log likelihood: -4618.760021
EM: Round [470] log likelihood: -4618.759029
EM: Round [471] log likelihood: -4618.758043
EM: Round [472] log likelihood: -4618.757061
EM: Round [473] log likelihood: -4618.756085
EM: Round [474] log likelihood: -4618.755115
EM: Round [475] log likelihood: -4618.754149
EM: Round [476] log likelihood: -4618.753189
EM: Round [477] log likelihood: -4618.752234
EM: Round [478] log likelihood: -4618.751283
EM: Round [479] log likelihood: -4618.750338
EM: Round [480] log likelihood: -4618.749398
EM: Round [481] log likelihood: -4618.748463
EM: Round [482] log likelihood: -4618.747533
EM: Round [483] log likelihood: -4618.746608
EM: Round [484] log likelihood: -4618.745688
EM: Round [485] log likelihood: -4618.744773
EM: Round [486] log likelihood: -4618.743862
EM: Round [487] log likelihood: -4618.742957
EM: Round [488] log likelihood: -4618.742056
EM: Round [489] log likelihood: -4618.741160
EM: Round [490] log likelihood: -4618.740269
EM: Round [491] log likelihood: -4618.739382
EM: Round [492] log likelihood: -4618.738501
EM: Round [493] log likelihood: -4618.737624
EM: Round [494] log likelihood: -4618.736751
EM: Round [495] log likelihood: -4618.735883
EM: Round [496] log likelihood: -4618.735020
EM: Round [497] log likelihood: -4618.734162
EM: Round [498] log likelihood: -4618.733307
EM: Round [499] log likelihood: -4618.732458
EM: Round [500] log likelihood: -4618.731613
EM: Round [501] log likelihood: -4618.730772
EM: Round [502] log likelihood: -4618.729936
EM: Round [503] log likelihood: -4618.729104
EM: Round [504] log likelihood: -4618.728277
EM: Round [505] log likelihood: -4618.727454
EM: Round [506] log likelihood: -4618.726635
EM: Round [507] log likelihood: -4618.725821
EM: Round [508] log likelihood: -4618.725011
EM: Round [509] log likelihood: -4618.724205
EM: Round [510] log likelihood: -4618.723403
EM: Round [511] log likelihood: -4618.722606
EM: Round [512] log likelihood: -4618.721813
EM: Round [513] log likelihood: -4618.721024
EM: Round [514] log likelihood: -4618.720239
EM: Round [515] log likelihood: -4618.719458
EM: Round [516] log likelihood: -4618.718682
EM: Round [517] log likelihood: -4618.717909
EM: Round [518] log likelihood: -4618.717141
EM: Round [519] log likelihood: -4618.716376
EM: Round [520] log likelihood: -4618.715616
EM: Round [521] log likelihood: -4618.714859
EM: Round [522] log likelihood: -4618.714107
EM: Round [523] log likelihood: -4618.713358
EM: Round [524] log likelihood: -4618.712614
EM: Round [525] log likelihood: -4618.711873
EM: Round [526] log likelihood: -4618.711136
EM: Round [527] log likelihood: -4618.710403
EM: Round [528] log likelihood: -4618.709674
EM: Round [529] log likelihood: -4618.708949
EM: Round [530] log likelihood: -4618.708227
EM: Round [531] log likelihood: -4618.707509
EM: Round [532] log likelihood: -4618.706795
EM: Round [533] log likelihood: -4618.706085
EM: Round [534] log likelihood: -4618.705378
EM: Round [535] log likelihood: -4618.704675
EM: Round [536] log likelihood: -4618.703976
EM: Round [537] log likelihood: -4618.703281
EM: Round [538] log likelihood: -4618.702589
EM: Round [539] log likelihood: -4618.701900
EM: Round [540] log likelihood: -4618.701215
EM: Round [541] log likelihood: -4618.700534
EM: Round [542] log likelihood: -4618.699856
EM: Round [543] log likelihood: -4618.699182
EM: Round [544] log likelihood: -4618.698512
EM: Round [545] log likelihood: -4618.697844
EM: Round [546] log likelihood: -4618.697181
EM: Round [547] log likelihood: -4618.696520
EM: Round [548] log likelihood: -4618.695864
EM: Round [549] log likelihood: -4618.695210
EM: Round [550] log likelihood: -4618.694560
EM: Round [551] log likelihood: -4618.693913
EM: Round [552] log likelihood: -4618.693270
EM: Round [553] log likelihood: -4618.692630
EM: Round [554] log likelihood: -4618.691993
EM: Round [555] log likelihood: -4618.691360
EM: Round [556] log likelihood: -4618.690730
EM: Round [557] log likelihood: -4618.690103
EM: Round [558] log likelihood: -4618.689480
EM: Round [559] log likelihood: -4618.688859
EM: Round [560] log likelihood: -4618.688242
EM: Round [561] log likelihood: -4618.687628
EM: Round [562] log likelihood: -4618.687017
EM: Round [563] log likelihood: -4618.686410
EM: Round [564] log likelihood: -4618.685805
EM: Round [565] log likelihood: -4618.685204
EM: Round [566] log likelihood: -4618.684606
EM: Round [567] log likelihood: -4618.684010
EM: Round [568] log likelihood: -4618.683418
EM: Round [569] log likelihood: -4618.682829
EM: Round [570] log likelihood: -4618.682243
EM: Round [571] log likelihood: -4618.681660
EM: Round [572] log likelihood: -4618.681080
EM: Round [573] log likelihood: -4618.680503
EM: Round [574] log likelihood: -4618.679929
EM: Round [575] log likelihood: -4618.679358
EM: Round [576] log likelihood: -4618.678790
EM: Round [577] log likelihood: -4618.678225
EM: Round [578] log likelihood: -4618.677662
EM: Round [579] log likelihood: -4618.677103
EM: Round [580] log likelihood: -4618.676546
EM: Round [581] log likelihood: -4618.675993
EM: Round [582] log likelihood: -4618.675442
EM: Round [583] log likelihood: -4618.674894
EM: Round [584] log likelihood: -4618.674349
EM: Round [585] log likelihood: -4618.673806
EM: Round [586] log likelihood: -4618.673267
EM: Round [587] log likelihood: -4618.672730
EM: Round [588] log likelihood: -4618.672196
EM: Round [589] log likelihood: -4618.671664
EM: Round [590] log likelihood: -4618.671136
EM: Round [591] log likelihood: -4618.670610
EM: Round [592] log likelihood: -4618.670087
EM: Round [593] log likelihood: -4618.669566
EM: Round [594] log likelihood: -4618.669048
EM: Round [595] log likelihood: -4618.668533
EM: Round [596] log likelihood: -4618.668020
EM: Round [597] log likelihood: -4618.667510
EM: Round [598] log likelihood: -4618.667003
EM: Round [599] log likelihood: -4618.666498
EM: Round [600] log likelihood: -4618.665996
EM: Round [601] log likelihood: -4618.665496
EM: Round [602] log likelihood: -4618.664999
EM: Round [603] log likelihood: -4618.664505
EM: Round [604] log likelihood: -4618.664013
EM: Round [605] log likelihood: -4618.663523
EM: Round [606] log likelihood: -4618.663036
EM: Round [607] log likelihood: -4618.662552
EM: Round [608] log likelihood: -4618.662070
EM: Round [609] log likelihood: -4618.661590
EM: Round [610] log likelihood: -4618.661113
EM: Round [611] log likelihood: -4618.660638
EM: Round [612] log likelihood: -4618.660166
EM: Round [613] log likelihood: -4618.659696
EM: Round [614] log likelihood: -4618.659229
EM: Round [615] log likelihood: -4618.658764
EM: Round [616] log likelihood: -4618.658301
EM: Round [617] log likelihood: -4618.657841
EM: Round [618] log likelihood: -4618.657383
EM: Round [619] log likelihood: -4618.656927
EM: Round [620] log likelihood: -4618.656473
EM: Round [621] log likelihood: -4618.656022
EM: Round [622] log likelihood: -4618.655574
EM: Round [623] log likelihood: -4618.655127
EM: Round [624] log likelihood: -4618.654683
EM: Round [625] log likelihood: -4618.654241
EM: Round [626] log likelihood: -4618.653801
EM: Round [627] log likelihood: -4618.653364
EM: Round [628] log likelihood: -4618.652928
EM: Round [629] log likelihood: -4618.652495
EM: Round [630] log likelihood: -4618.652064
EM: Round [631] log likelihood: -4618.651636
EM: Round [632] log likelihood: -4618.651209
EM: Round [633] log likelihood: -4618.650785
EM: Round [634] log likelihood: -4618.650363
EM: Round [635] log likelihood: -4618.649943
EM: Round [636] log likelihood: -4618.649525
EM: Round [637] log likelihood: -4618.649109
EM: Round [638] log likelihood: -4618.648695
EM: Round [639] log likelihood: -4618.648284
EM: Round [640] log likelihood: -4618.647874
EM: Round [641] log likelihood: -4618.647467
EM: Round [642] log likelihood: -4618.647061
EM: Round [643] log likelihood: -4618.646658
EM: Round [644] log likelihood: -4618.646257
EM: Round [645] log likelihood: -4618.645858
EM: Round [646] log likelihood: -4618.645460
EM: Round [647] log likelihood: -4618.645065
EM: Round [648] log likelihood: -4618.644672
EM: Round [649] log likelihood: -4618.644281
EM: Round [650] log likelihood: -4618.643891
EM: Round [651] log likelihood: -4618.643504
EM: Round [652] log likelihood: -4618.643119
EM: Round [653] log likelihood: -4618.642735
EM: Round [654] log likelihood: -4618.642354
EM: Round [655] log likelihood: -4618.641974
EM: Round [656] log likelihood: -4618.641597
EM: Round [657] log likelihood: -4618.641221
EM: Round [658] log likelihood: -4618.640847
EM: Round [659] log likelihood: -4618.640475
EM: Round [660] log likelihood: -4618.640105
EM: Round [661] log likelihood: -4618.639737
EM: Round [662] log likelihood: -4618.639371
EM: Round [663] log likelihood: -4618.639006
EM: Round [664] log likelihood: -4618.638644
EM: Round [665] log likelihood: -4618.638283
EM: Round [666] log likelihood: -4618.637924
EM: Round [667] log likelihood: -4618.637567
EM: Round [668] log likelihood: -4618.637211
EM: Round [669] log likelihood: -4618.636858
EM: Round [670] log likelihood: -4618.636506
EM: Round [671] log likelihood: -4618.636156
EM: Round [672] log likelihood: -4618.635808
EM: Round [673] log likelihood: -4618.635461
EM: Round [674] log likelihood: -4618.635116
EM: Round [675] log likelihood: -4618.634773
EM: Round [676] log likelihood: -4618.634432
EM: Round [677] log likelihood: -4618.634092
EM: Round [678] log likelihood: -4618.633755
EM: Round [679] log likelihood: -4618.633418
EM: Round [680] log likelihood: -4618.633084
EM: Round [681] log likelihood: -4618.632751
EM: Round [682] log likelihood: -4618.632420
EM: Round [683] log likelihood: -4618.632090
EM: Round [684] log likelihood: -4618.631762
EM: Round [685] log likelihood: -4618.631436
EM: Round [686] log likelihood: -4618.631112
EM: Round [687] log likelihood: -4618.630789
EM: Round [688] log likelihood: -4618.630468
EM: Round [689] log likelihood: -4618.630148
EM: Round [690] log likelihood: -4618.629830
EM: Round [691] log likelihood: -4618.629513
EM: Round [692] log likelihood: -4618.629198
EM: Round [693] log likelihood: -4618.628885
EM: Round [694] log likelihood: -4618.628573
EM: Round [695] log likelihood: -4618.628263
EM: Round [696] log likelihood: -4618.627954
EM: Round [697] log likelihood: -4618.627647
EM: Round [698] log likelihood: -4618.627342
EM: Round [699] log likelihood: -4618.627038
EM: Round [700] log likelihood: -4618.626735
EM: Round [701] log likelihood: -4618.626434
EM: Round [702] log likelihood: -4618.626135
EM: Round [703] log likelihood: -4618.625837
EM: Round [704] log likelihood: -4618.625540
EM: Round [705] log likelihood: -4618.625245
EM: Round [706] log likelihood: -4618.624952
EM: Round [707] log likelihood: -4618.624660
EM: Round [708] log likelihood: -4618.624369
EM: Round [709] log likelihood: -4618.624080
EM: Round [710] log likelihood: -4618.623792
EM: Round [711] log likelihood: -4618.623506
EM: Round [712] log likelihood: -4618.623221
EM: Round [713] log likelihood: -4618.622938
EM: Round [714] log likelihood: -4618.622656
EM: Round [715] log likelihood: -4618.622375
EM: Round [716] log likelihood: -4618.622096
EM: Round [717] log likelihood: -4618.621818
EM: Round [718] log likelihood: -4618.621542
EM: Round [719] log likelihood: -4618.621267
EM: Round [720] log likelihood: -4618.620993
EM: Round [721] log likelihood: -4618.620721
EM: Round [722] log likelihood: -4618.620450
EM: Round [723] log likelihood: -4618.620181
EM: Round [724] log likelihood: -4618.619912
EM: Round [725] log likelihood: -4618.619646
EM: Round [726] log likelihood: -4618.619380
EM: Round [727] log likelihood: -4618.619116
EM: Round [728] log likelihood: -4618.618853
EM: Round [729] log likelihood: -4618.618591
EM: Round [730] log likelihood: -4618.618331
EM: Round [731] log likelihood: -4618.618072
EM: Round [732] log likelihood: -4618.617814
EM: Round [733] log likelihood: -4618.617558
EM: Round [734] log likelihood: -4618.617303
EM: Round [735] log likelihood: -4618.617049
EM: Round [736] log likelihood: -4618.616796
EM: Round [737] log likelihood: -4618.616545
EM: Round [738] log likelihood: -4618.616295
EM: Round [739] log likelihood: -4618.616046
EM: Round [740] log likelihood: -4618.615799
EM: Round [741] log likelihood: -4618.615552
EM: Round [742] log likelihood: -4618.615307
EM: Round [743] log likelihood: -4618.615063
EM: Round [744] log likelihood: -4618.614820
EM: Round [745] log likelihood: -4618.614579
EM: Round [746] log likelihood: -4618.614339
EM: Round [747] log likelihood: -4618.614099
EM: Round [748] log likelihood: -4618.613862
EM: Round [749] log likelihood: -4618.613625
EM: Round [750] log likelihood: -4618.613389
EM: Round [751] log likelihood: -4618.613155
EM: Round [752] log likelihood: -4618.612922
EM: Round [753] log likelihood: -4618.612690
EM: Round [754] log likelihood: -4618.612459
EM: Round [755] log likelihood: -4618.612229
EM: Round [756] log likelihood: -4618.612000
EM: Round [757] log likelihood: -4618.611773
EM: Round [758] log likelihood: -4618.611547
EM: Round [759] log likelihood: -4618.611321
EM: Round [760] log likelihood: -4618.611097
EM: Round [761] log likelihood: -4618.610874
EM: Round [762] log likelihood: -4618.610652
EM: Round [763] log likelihood: -4618.610432
EM: Round [764] log likelihood: -4618.610212
EM: Round [765] log likelihood: -4618.609993
EM: Round [766] log likelihood: -4618.609776
EM: Round [767] log likelihood: -4618.609559
EM: Round [768] log likelihood: -4618.609344
EM: Round [769] log likelihood: -4618.609130
EM: Round [770] log likelihood: -4618.608917
EM: Round [771] log likelihood: -4618.608704
EM: Round [772] log likelihood: -4618.608493
EM: Round [773] log likelihood: -4618.608283
EM: Round [774] log likelihood: -4618.608074
EM: Round [775] log likelihood: -4618.607866
EM: Round [776] log likelihood: -4618.607659
EM: Round [777] log likelihood: -4618.607453
EM: Round [778] log likelihood: -4618.607249
EM: Round [779] log likelihood: -4618.607045
EM: Round [780] log likelihood: -4618.606842
EM: Round [781] log likelihood: -4618.606640
EM: Round [782] log likelihood: -4618.606439
EM: Round [783] log likelihood: -4618.606239
EM: Round [784] log likelihood: -4618.606040
EM: Round [785] log likelihood: -4618.605842
EM: Round [786] log likelihood: -4618.605645
EM: Round [787] log likelihood: -4618.605450
EM: Round [788] log likelihood: -4618.605255
EM: Round [789] log likelihood: -4618.605061
EM: Round [790] log likelihood: -4618.604868
EM: Round [791] log likelihood: -4618.604675
EM: Round [792] log likelihood: -4618.604484
EM: Round [793] log likelihood: -4618.604294
EM: Round [794] log likelihood: -4618.604105
EM: Round [795] log likelihood: -4618.603917
EM: Round [796] log likelihood: -4618.603729
EM: Round [797] log likelihood: -4618.603543
EM: Round [798] log likelihood: -4618.603357
EM: Round [799] log likelihood: -4618.603173
EM: Round [800] log likelihood: -4618.602989
EM: Round [801] log likelihood: -4618.602806
EM: Round [802] log likelihood: -4618.602624
EM: Round [803] log likelihood: -4618.602443
EM: Round [804] log likelihood: -4618.602263
EM: Round [805] log likelihood: -4618.602084
EM: Round [806] log likelihood: -4618.601906
EM: Round [807] log likelihood: -4618.601728
EM: Round [808] log likelihood: -4618.601552
EM: Round [809] log likelihood: -4618.601376
EM: Round [810] log likelihood: -4618.601201
EM: Round [811] log likelihood: -4618.601027
EM: Round [812] log likelihood: -4618.600854
EM: Round [813] log likelihood: -4618.600682
EM: Round [814] log likelihood: -4618.600510
EM: Round [815] log likelihood: -4618.600340
EM: Round [816] log likelihood: -4618.600170
EM: Round [817] log likelihood: -4618.600001
EM: Round [818] log likelihood: -4618.599833
EM: Round [819] log likelihood: -4618.599666
EM: Round [820] log likelihood: -4618.599500
EM: Round [821] log likelihood: -4618.599334
EM: Round [822] log likelihood: -4618.599169
EM: Round [823] log likelihood: -4618.599005
EM: Round [824] log likelihood: -4618.598842
EM: Round [825] log likelihood: -4618.598680
EM: Round [826] log likelihood: -4618.598518
EM: Round [827] log likelihood: -4618.598358
EM: Round [828] log likelihood: -4618.598198
EM: Round [829] log likelihood: -4618.598039
EM: Round [830] log likelihood: -4618.597880
EM: Round [831] log likelihood: -4618.597723
EM: Round [832] log likelihood: -4618.597566
EM: Round [833] log likelihood: -4618.597410
EM: Round [834] log likelihood: -4618.597255
EM: Round [835] log likelihood: -4618.597100
EM: Round [836] log likelihood: -4618.596947
EM: Round [837] log likelihood: -4618.596794
EM: Round [838] log likelihood: -4618.596641
EM: Round [839] log likelihood: -4618.596490
EM: Round [840] log likelihood: -4618.596339
EM: Round [841] log likelihood: -4618.596189
EM: Round [842] log likelihood: -4618.596040
EM: Round [843] log likelihood: -4618.595892
EM: Round [844] log likelihood: -4618.595744
EM: Round [845] log likelihood: -4618.595597
EM: Round [846] log likelihood: -4618.595450
EM: Round [847] log likelihood: -4618.595305
EM: Round [848] log likelihood: -4618.595160
EM: Round [849] log likelihood: -4618.595016
EM: Round [850] log likelihood: -4618.594872
EM: Round [851] log likelihood: -4618.594730
EM: Round [852] log likelihood: -4618.594588
EM: Round [853] log likelihood: -4618.594446
EM: Round [854] log likelihood: -4618.594306
EM: Round [855] log likelihood: -4618.594166
EM: Round [856] log likelihood: -4618.594026
EM: Round [857] log likelihood: -4618.593888
EM: Round [858] log likelihood: -4618.593750
EM: Round [859] log likelihood: -4618.593613
EM: Round [860] log likelihood: -4618.593476
EM: Round [861] log likelihood: -4618.593340
EM: Round [862] log likelihood: -4618.593205
EM: Round [863] log likelihood: -4618.593071
EM: Round [864] log likelihood: -4618.592937
EM: Round [865] log likelihood: -4618.592803
EM: Round [866] log likelihood: -4618.592671
EM: Round [867] log likelihood: -4618.592539
EM: Round [868] log likelihood: -4618.592408
EM: Round [869] log likelihood: -4618.592277
EM: Round [870] log likelihood: -4618.592147
EM: Round [871] log likelihood: -4618.592018
EM: Round [872] log likelihood: -4618.591889
EM: Round [873] log likelihood: -4618.591761
EM: Round [874] log likelihood: -4618.591634
EM: Round [875] log likelihood: -4618.591507
EM: Round [876] log likelihood: -4618.591381
EM: Round [877] log likelihood: -4618.591255
EM: Round [878] log likelihood: -4618.591130
EM: Round [879] log likelihood: -4618.591006
EM: Round [880] log likelihood: -4618.590882
EM: Round [881] log likelihood: -4618.590759
EM: Round [882] log likelihood: -4618.590636
EM: Round [883] log likelihood: -4618.590515
EM: Round [884] log likelihood: -4618.590393
EM: Round [885] log likelihood: -4618.590272
EM: Round [886] log likelihood: -4618.590152
EM: Round [887] log likelihood: -4618.590033
EM: Round [888] log likelihood: -4618.589914
EM: Round [889] log likelihood: -4618.589796
EM: Round [890] log likelihood: -4618.589678
EM: Round [891] log likelihood: -4618.589561
EM: Round [892] log likelihood: -4618.589444
EM: Round [893] log likelihood: -4618.589328
EM: Round [894] log likelihood: -4618.589212
EM: Round [895] log likelihood: -4618.589097
EM: Round [896] log likelihood: -4618.588983
EM: Round [897] log likelihood: -4618.588869
EM: Round [898] log likelihood: -4618.588756
EM: Round [899] log likelihood: -4618.588643
EM: Round [900] log likelihood: -4618.588531
EM: Round [901] log likelihood: -4618.588420
EM: Round [902] log likelihood: -4618.588309
EM: Round [903] log likelihood: -4618.588198
EM: Round [904] log likelihood: -4618.588088
EM: Round [905] log likelihood: -4618.587979
EM: Round [906] log likelihood: -4618.587870
EM: Round [907] log likelihood: -4618.587762
EM: Round [908] log likelihood: -4618.587654
EM: Round [909] log likelihood: -4618.587547
EM: Round [910] log likelihood: -4618.587440
EM: Round [911] log likelihood: -4618.587334
EM: Round [912] log likelihood: -4618.587228
EM: Round [913] log likelihood: -4618.587123
EM: Round [914] log likelihood: -4618.587018
EM: Round [915] log likelihood: -4618.586914
EM: Round [916] log likelihood: -4618.586810
EM: Round [917] log likelihood: -4618.586707
EM: Round [918] log likelihood: -4618.586605
EM: Round [919] log likelihood: -4618.586502
EM: Round [920] log likelihood: -4618.586401
EM: Round [921] log likelihood: -4618.586300
EM: Round [922] log likelihood: -4618.586199
EM: Round [923] log likelihood: -4618.586099
EM: Round [924] log likelihood: -4618.585999
EM: Stopping iterations at round 924 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa > /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir
-done, see /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2866.976802
EM: Round [1] log likelihood: -2866.841495
EM: Round [2] log likelihood: -2866.841126
EM: Round [3] log likelihood: -2866.841124
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296712379
Execution Time = 5.71 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.5gGev74vOT/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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.5gGev74vOT/fi_workdir/microH.dat
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.5gGev74vOT/fi_workdir/microH.dat /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/fi_workdir/microH.dat /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.5gGev74vOT --json_outfile /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.5gGev74vOT --json_outfile /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.5gGev74vOT/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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1 --html_output /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-7f9674-R1_A23YTGFLT4_1 --html_output /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259028.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.5gGev74vOT/ctat_genome_lib_build_dir > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.5gGev74vOT/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory