Done.
-parsing GTF file: /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.k4x1dSR1c2/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.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00671_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00671_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:08:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_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]   -done parsing /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'exons hit < 2' => 1,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 151,
          'low complexity anchor region' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
          ' ** passed ** ' => 1662,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 6,
          'num genes matched < 2' => 37,
          'small anchor length' => 39,
          'per_id < 96' => 2545,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
          'excessive soft clipping' => 4299,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_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]   -fusion SPANNING read extraction for scaff: ACSS1--MRPS11P1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: ACSS1--AL133465.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: ACSS1--RN7SL607P

[1000]   -fusion SPANNING read extraction for scaff: AL669831.4--SEPTIN14

[1000]   -fusion SPANNING read extraction for scaff: AP006294.2--ENPP7P3

[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]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

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

[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]   -fusion SPANNING read extraction for scaff: PGBD2--ZNF692

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PPP2R2B--STK32A

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

[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: SCRN3--SLC44A5

[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]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   -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]   
[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]   -fusion SPANNING read extraction for scaff: TCERG1--PPP2R2B

[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]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[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]   -fusion SPANNING read extraction for scaff: VWA8--LINC01160
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 3325
        };
EM: Starting log likelihood: -2515.442392
EM: Round [1] log likelihood: -2506.233678
EM: Round [2] log likelihood: -2506.102609
EM: Round [3] log likelihood: -2506.102009
EM: Round [4] log likelihood: -2506.102006
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.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.k4x1dSR1c2/fi_workdir/tih_rna_sample_00671_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2321.366747
EM: Round [1] log likelihood: -2320.637859
EM: Round [2] log likelihood: -2320.637563
EM: Round [3] log likelihood: -2320.637562
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1_1.fastp.fastq.gz: 296369001
Warning - not locating file: /tmp/nxf.k4x1dSR1c2/tih_rna_sample_00671_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000230092.7]
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 [ENSG00000284639.1]
WARNING, no entry stored in dbm for [ENSG00000248618.1]
WARNING, no entry stored in dbm for [ENSG00000231346.5]
ls: cannot access 'IGV_inputs': No such file or directory