Error, strand conflict in gtf info for chr1 ENSEMBL exon 43716467 43716556 . + . gene_id "U6^ENSG00000283414.1"; transcript_id "ENST00000637979.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.104-201"; exon_number 1; exon_id "ENSE00003791911.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283414.1"; orig_coord_info "chr1,43716467,43716556,+";
Error, strand conflict in gtf info for chr1 ENSEMBL exon 180758722 180758817 . + . gene_id "U6^ENSG00000283575.1"; transcript_id "ENST00000636407.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.114-201"; exon_number 1; exon_id "ENSE00003794679.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283575.1"; orig_coord_info "chr1,180758722,180758817,+";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 47781379 47781465 . + . gene_id "U6^ENSG00000283502.1"; transcript_id "ENST00000636749.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.109-201"; exon_number 1; exon_id "ENSE00003797274.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283502.1"; orig_coord_info "chr2,47781379,47781465,+";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 88367793 88367862 . - . gene_id "U6^ENSG00000283262.1"; transcript_id "ENST00000636931.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.95-201"; exon_number 1; exon_id "ENSE00003794432.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283262.1"; orig_coord_info "chr2,88367793,88367862,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 129819777 129819876 . + . gene_id "U6^ENSG00000283509.1"; transcript_id "ENST00000637725.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.110-201"; exon_number 1; exon_id "ENSE00003800884.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283509.1"; orig_coord_info "chr3,129819777,129819876,+";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 139388277 139388364 . + . gene_id "U6^ENSG00000283418.1"; transcript_id "ENST00000637379.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.105-201"; exon_number 1; exon_id "ENSE00003796411.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283418.1"; orig_coord_info "chr3,139388277,139388364,+";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 13051342 13051411 . + . gene_id "U6^ENSG00000283271.1"; transcript_id "ENST00000636425.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.96-201"; exon_number 1; exon_id "ENSE00003794917.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283271.1"; orig_coord_info "chr4,13051342,13051411,+";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 29510635 29510737 . + . gene_id "U6^ENSG00000283666.1"; transcript_id "ENST00000636045.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.115-201"; exon_number 1; exon_id "ENSE00003798657.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283666.1"; orig_coord_info "chr4,29510635,29510737,+";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 48109353 48109410 . - . gene_id "U6^ENSG00000283499.1"; transcript_id "ENST00000637764.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.108-201"; exon_number 1; exon_id "ENSE00003792913.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283499.1"; orig_coord_info "chr4,48109353,48109410,-";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 70848136 70848218 . - . gene_id "U6^ENSG00000283313.1"; transcript_id "ENST00000637524.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.99-201"; exon_number 1; exon_id "ENSE00003794269.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283313.1"; orig_coord_info "chr4,70848136,70848218,-";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 135315418 135315522 . - . gene_id "U6^ENSG00000283432.1"; transcript_id "ENST00000636360.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.106-201"; exon_number 1; exon_id "ENSE00003800825.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283432.1"; orig_coord_info "chr4,135315418,135315522,-";
Error, chr discrepancy in gtf info for chr9 ENSEMBL exon 64082429 64082534 . + . gene_id "U6^ENSG00000275068.1"; transcript_id "ENST00000618523.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.48-201"; exon_number 1; exon_id "ENSE00003712247.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275068.1"; orig_coord_info "chr9,64082429,64082534,+";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 102868421 102868519 . + . gene_id "U6^ENSG00000283337.1"; transcript_id "ENST00000636230.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.100-201"; exon_number 1; exon_id "ENSE00003800313.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283337.1"; orig_coord_info "chr10,102868421,102868519,+";
Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 87648489 87648549 . - . gene_id "U6^ENSG00000283412.1"; transcript_id "ENST00000637085.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.103-201"; exon_number 1; exon_id "ENSE00003793834.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283412.1"; orig_coord_info "chr11,87648489,87648549,-";
Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 132525809 132525887 . + . gene_id "U6^ENSG00000283489.1"; transcript_id "ENST00000637108.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.107-201"; exon_number 1; exon_id "ENSE00003795495.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283489.1"; orig_coord_info "chr11,132525809,132525887,+";
Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 31366288 31366366 . + . gene_id "U6^ENSG00000283256.1"; transcript_id "ENST00000635778.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.94-201"; exon_number 1; exon_id "ENSE00003799600.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283256.1"; orig_coord_info "chr12,31366288,31366366,+";
Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 45554590 45554659 . - . gene_id "U6^ENSG00000283545.1"; transcript_id "ENST00000384129.2"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.112-201"; exon_number 1; exon_id "ENSE00001808939.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283545.1"; orig_coord_info "chr12,45554590,45554659,-";
Error, chr discrepancy in gtf info for chr13 ENSEMBL exon 18418526 18418632 . + . gene_id "U6^ENSG00000276183.1"; transcript_id "ENST00000615686.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.59-201"; exon_number 1; exon_id "ENSE00003719890.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276183.1"; orig_coord_info "chr13,18418526,18418632,+";
Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 24352057 24352157 . - . gene_id "U6^ENSG00000283290.1"; transcript_id "ENST00000636904.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.97-201"; exon_number 1; exon_id "ENSE00003800280.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283290.1"; orig_coord_info "chr14,24352057,24352157,-";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 21428879 21428985 . - . gene_id "U6^ENSG00000275174.1"; transcript_id "ENST00000612037.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.50-201"; exon_number 1; exon_id "ENSE00003750231.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275174.1"; orig_coord_info "chr15,21428879,21428985,-";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 65843484 65843558 . + . gene_id "U6^ENSG00000283249.1"; transcript_id "ENST00000636829.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.93-201"; exon_number 1; exon_id "ENSE00003798324.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283249.1"; orig_coord_info "chr15,65843484,65843558,+";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 98026042 98026139 . + . gene_id "U6^ENSG00000283372.1"; transcript_id "ENST00000637737.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.102-201"; exon_number 1; exon_id "ENSE00003800921.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283372.1"; orig_coord_info "chr15,98026042,98026139,+";
Error, chr discrepancy in gtf info for chr16 ENSEMBL exon 72376704 72376760 . + . gene_id "U6^ENSG00000283564.1"; transcript_id "ENST00000637761.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.113-201"; exon_number 1; exon_id "ENSE00003793842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283564.1"; orig_coord_info "chr16,72376704,72376760,+";
Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 90796 90899 . - . gene_id "U6^ENSG00000277613.1"; transcript_id "ENST00000620287.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.70-201"; exon_number 1; exon_id "ENSE00003744841.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277613.1"; orig_coord_info "chr17,90796,90899,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30713240 30713346 . - . gene_id "U6^ENSG00000274385.1"; transcript_id "ENST00000618440.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.42-201"; exon_number 1; exon_id "ENSE00003712066.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000274385.1"; orig_coord_info "chr20,30713240,30713346,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 35769785 35769867 . - . gene_id "U6^ENSG00000283527.1"; transcript_id "ENST00000636093.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.111-201"; exon_number 1; exon_id "ENSE00003795784.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283527.1"; orig_coord_info "chr20,35769785,35769867,-";
Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 28743208 28743291 . + . gene_id "U6^ENSG00000283300.1"; transcript_id "ENST00000637157.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.98-201"; exon_number 1; exon_id "ENSE00003800948.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283300.1"; orig_coord_info "chr21,28743208,28743291,+";
Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 15273855 15273961 . + . gene_id "U6^ENSG00000276138.1"; transcript_id "ENST00000613107.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.58-201"; exon_number 1; exon_id "ENSE00003736970.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276138.1"; orig_coord_info "chr22,15273855,15273961,+";
Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 16141767 16141872 . + . gene_id "U6^ENSG00000278188.1"; transcript_id "ENST00000612550.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.81-201"; exon_number 1; exon_id "ENSE00003714392.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000278188.1"; orig_coord_info "chr22,16141767,16141872,+";
Error, chr discrepancy in gtf info for chrX ENSEMBL exon 86481028 86481130 . + . gene_id "U6^ENSG00000277717.1"; transcript_id "ENST00000619194.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.73-201"; exon_number 1; exon_id "ENSE00003738865.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277717.1"; orig_coord_info "chrX,86481028,86481130,+";
Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589.
main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417
main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"..., "/tmp/nxf.hpsEvEZN4q/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214
eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210
Done.
-parsing GTF file: /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.hpsEvEZN4q/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.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:42:35 : INFO : Done.
-parsing GTF file: /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[3830000] -done parsing /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 23319,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'small anchor length' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
'num genes matched < 2' => 418,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 114,
' ** passed ** ' => 5305,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 58,
'low complexity anchor region' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 174,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 474,
'per_id < 96' => 12612
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[1073000] -fusion SPANNING read extraction for scaff: ACTBP6--ACTB
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[138000] -fusion SPANNING read extraction for scaff: ATAD2--AL365295.1
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[109000] -fusion SPANNING read extraction for scaff: FRMD6--ABHD12B
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[29000] -fusion SPANNING read extraction for scaff: FTO--FRG1GP
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[43000] -fusion SPANNING read extraction for scaff: IGF1R--FAM169B
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[36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC092745.5
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[36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC024255.1
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[36000] -fusion SPANNING read extraction for scaff: NDUFA9--AC012150.1
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[933000] -fusion SPANNING read extraction for scaff: SAA2--MT-RNR2
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[98000] -fusion SPANNING read extraction for scaff: TATDN1--NSMCE2
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[20000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[17000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 42105
};
EM: Starting log likelihood: -7193.100127
EM: Round [1] log likelihood: -7163.479190
EM: Round [2] log likelihood: -7163.069547
EM: Round [3] log likelihood: -7163.067557
EM: Round [4] log likelihood: -7163.067550
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-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.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-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.hpsEvEZN4q/fi_workdir/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6568.069392
EM: Round [1] log likelihood: -6540.915901
EM: Round [2] log likelihood: -6540.432046
EM: Round [3] log likelihood: -6540.429357
EM: Round [4] log likelihood: -6540.429347
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296664875
Warning - not locating file: /tmp/nxf.hpsEvEZN4q/aih-tih-sc-a8a787-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000251448.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
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 [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000286895.1]
WARNING, no entry stored in dbm for [ENSG00000286895.1]
WARNING, no entry stored in dbm for [ENSG00000286895.1]
WARNING, no entry stored in dbm for [ENSG00000249816.7]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
ls: cannot access 'IGV_inputs': No such file or directory