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/f3/ef332670617ccbf31b49b11cc0b830/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/cb5c4b183349561367b746d2c6cdd5/GM24385_0001_RNA_0001_23H5VFLT4_s24.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/a361851e75629faef8a9cf2d392fc5/GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/cb5c4b183349561367b746d2c6cdd5/GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/ef332670617ccbf31b49b11cc0b830/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/cb5c4b183349561367b746d2c6cdd5/GM24385_0001_RNA_0001_23H5VFLT4_s24.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 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[6060000], rate=20200000.00/min [6070000], rate=20233333.33/min [6080000], rate=20266666.67/min [6090000], rate=20300000.00/min [6100000], rate=20333333.33/min [6110000], rate=19294736.84/min [6120000], rate=19326315.79/min [6130000], rate=19357894.74/min [6140000], rate=19389473.68/min [6150000], rate=19421052.63/min [6160000], rate=19452631.58/min [6170000], rate=19484210.53/min [6180000], rate=19515789.47/min [6190000], rate=19547368.42/min [6200000], rate=19578947.37/min [6210000], rate=19610526.32/min [6220000], rate=19642105.26/min [6230000], rate=19673684.21/min [6240000], rate=19705263.16/min [6250000], rate=19736842.11/min [6260000], rate=19768421.05/min [6270000], rate=19800000.00/min [6280000], rate=19831578.95/min [6290000], rate=19863157.89/min [6300000], rate=19894736.84/min [6310000], rate=19926315.79/min [6320000], rate=19957894.74/min [6330000], rate=19989473.68/min [6340000], rate=20021052.63/min [6350000], rate=20052631.58/min [6360000], rate=20084210.53/min [6370000], rate=20115789.47/min [6380000], rate=20147368.42/min [6390000], rate=20178947.37/min [6400000], rate=20210526.32/min [6410000], rate=20242105.26/min [6420000], rate=20273684.21/min [6430000], rate=20305263.16/min [6440000], rate=19320000.00/min [6450000], rate=19350000.00/min [6460000], rate=19380000.00/min [6470000], rate=19410000.00/min [6480000], rate=19440000.00/min [6490000], rate=19470000.00/min [6500000], rate=19500000.00/min [6510000], rate=19530000.00/min [6520000], rate=19560000.00/min [6530000], rate=19590000.00/min [6540000], rate=19620000.00/min [6550000], rate=19650000.00/min [6560000], rate=19680000.00/min [6570000], rate=19710000.00/min [6580000], rate=19740000.00/min [6590000], rate=19770000.00/min [6600000], rate=19800000.00/min [6610000], rate=19830000.00/min [6620000], rate=19860000.00/min [6630000], rate=19890000.00/min [6640000], rate=19920000.00/min [6650000], rate=19950000.00/min [6660000], rate=19980000.00/min [6670000], rate=20010000.00/min [6680000], rate=20040000.00/min [6690000], rate=20070000.00/min [6700000], rate=20100000.00/min [6710000], rate=20130000.00/min [6720000], rate=20160000.00/min [6730000], rate=20190000.00/min [6740000], rate=20220000.00/min [6750000], rate=20250000.00/min [6760000], rate=20280000.00/min [6770000], rate=20310000.00/min [6780000], rate=20340000.00/min [6790000], rate=19400000.00/min [6800000], rate=19428571.43/min [6810000], rate=19457142.86/min [6820000], rate=19485714.29/min [6830000], rate=19514285.71/min [6840000], rate=19542857.14/min [6850000], rate=19571428.57/min [6860000], rate=19600000.00/min [6870000], rate=19628571.43/min [6880000], rate=19657142.86/min [6890000], rate=19685714.29/min [6900000], rate=19714285.71/min [6910000], rate=19742857.14/min [6920000], rate=19771428.57/min [6930000], rate=19800000.00/min [6940000], rate=19828571.43/min [6950000], rate=19857142.86/min [6960000], rate=19885714.29/min [6970000], rate=19914285.71/min [6980000], rate=19942857.14/min [6990000], rate=19971428.57/min [7000000], rate=20000000.00/min [7010000], rate=20028571.43/min [7020000], rate=20057142.86/min [7030000], rate=20085714.29/min [7040000], rate=20114285.71/min [7050000], rate=20142857.14/min [7060000], rate=20171428.57/min [7070000], rate=20200000.00/min [7080000], rate=20228571.43/min [7090000], rate=20257142.86/min [7100000], rate=20285714.29/min [7110000], rate=20314285.71/min [7120000], rate=20342857.14/min [7130000], rate=20371428.57/min [7140000], rate=19472727.27/min [7150000], rate=19500000.00/min [7160000], rate=19527272.73/min [7170000], rate=19554545.45/min [7180000], rate=19581818.18/min [7190000], rate=19609090.91/min [7200000], rate=19636363.64/min [7210000], rate=19663636.36/min [7220000], rate=19690909.09/min [7230000], rate=19718181.82/min [7240000], rate=19745454.55/min [7250000], rate=19772727.27/min [7260000], rate=19800000.00/min [7270000], rate=19827272.73/min [7280000], rate=19854545.45/min [7290000], rate=19881818.18/min [7300000], rate=19909090.91/min [7310000], rate=19936363.64/min [7320000], rate=19963636.36/min [7330000], rate=19990909.09/min [7340000], rate=20018181.82/min [7350000], rate=20045454.55/min [7360000], rate=20072727.27/min [7370000], rate=20100000.00/min [7380000], rate=20127272.73/min [7390000], rate=20154545.45/min [7400000], rate=20181818.18/min [7410000], rate=20209090.91/min [7420000], rate=20236363.64/min [7430000], rate=20263636.36/min [7440000], rate=20290909.09/min [7450000], rate=20318181.82/min [7460000], rate=20345454.55/min [7470000], rate=19486956.52/min [7480000], rate=19513043.48/min [7490000], rate=19539130.43/min [7500000], rate=19565217.39/min [7510000], rate=19591304.35/min [7520000], rate=19617391.30/min [7530000], rate=19643478.26/min [7540000], rate=19669565.22/min [7550000], rate=19695652.17/min [7560000], rate=19721739.13/min [7570000], rate=19747826.09/min [7580000], rate=19773913.04/min [7590000], rate=19800000.00/min [7600000], rate=19826086.96/min [7610000], rate=19852173.91/min [7620000], rate=19878260.87/min [7630000], rate=19904347.83/min [7640000], rate=19930434.78/min [7650000], rate=19956521.74/min [7660000], rate=19982608.70/min [7670000], rate=20008695.65/min [7680000], rate=20034782.61/min [7690000], rate=20060869.57/min [7700000], rate=20086956.52/min [7710000], rate=20113043.48/min [7720000], rate=20139130.43/min [7730000], rate=20165217.39/min [7740000], rate=20191304.35/min [7750000], rate=20217391.30/min [7760000], rate=20243478.26/min [7770000], rate=20269565.22/min [7780000], rate=20295652.17/min [7790000], rate=19475000.00/min [7800000], rate=19500000.00/min [7810000], rate=19525000.00/min [7820000], rate=19550000.00/min [7830000], rate=19575000.00/min [7840000], rate=19600000.00/min [7850000], rate=19625000.00/min [7860000], rate=19650000.00/min [7870000], rate=19675000.00/min [7880000], rate=19700000.00/min [7890000], rate=19725000.00/min [7900000], rate=19750000.00/min [7910000], rate=19775000.00/min [7920000], rate=19800000.00/min [7930000], rate=19825000.00/min [7940000], rate=19850000.00/min [7950000], rate=19875000.00/min [7960000], rate=19900000.00/min [7970000], rate=19925000.00/min [7980000], rate=19950000.00/min [7990000], rate=19975000.00/min [8000000], rate=20000000.00/min [8010000], rate=20025000.00/min [8020000], rate=20050000.00/min [8030000], rate=20075000.00/min [8040000], rate=20100000.00/min [8050000], rate=20125000.00/min [8060000], rate=20150000.00/min [8070000], rate=20175000.00/min [8080000], rate=20200000.00/min [8090000], rate=20225000.00/min [8100000], rate=20250000.00/min [8110000], rate=20275000.00/min [8120000], rate=20300000.00/min [8130000], rate=19512000.00/min [8140000], rate=19536000.00/min [8150000], rate=19560000.00/min [8160000], rate=19584000.00/min [8170000], rate=19608000.00/min [8180000], rate=19632000.00/min [8190000], rate=19656000.00/min [8200000], rate=19680000.00/min [8210000], rate=19704000.00/min [8220000], rate=19728000.00/min [8230000], rate=19752000.00/min [8240000], rate=19776000.00/min [8250000], rate=19800000.00/min [8260000], rate=19824000.00/min [8270000], rate=19848000.00/min [8280000], rate=19872000.00/min [8290000], rate=19896000.00/min [8300000], rate=19920000.00/min [8310000], rate=19944000.00/min [8320000], rate=19968000.00/min [8330000], rate=19992000.00/min [8340000], rate=20016000.00/min [8350000], rate=20040000.00/min [8360000], rate=20064000.00/min [8370000], rate=20088000.00/min [8380000], rate=20112000.00/min [8390000], rate=20136000.00/min [8400000], rate=20160000.00/min [8410000], rate=20184000.00/min [8420000], rate=20208000.00/min [8430000], rate=20232000.00/min [8440000], rate=20256000.00/min [8450000], rate=20280000.00/min [8460000], rate=20304000.00/min [8470000], rate=20328000.00/min [8480000], rate=19569230.77/min [8490000], rate=19592307.69/min [8500000], rate=19615384.62/min [8510000], rate=19638461.54/min [8520000], rate=19661538.46/min [8530000], rate=19684615.38/min [8540000], rate=19707692.31/min [8550000], rate=19730769.23/min [8560000], rate=19753846.15/min [8570000], rate=19776923.08/min [8580000], rate=19800000.00/min [8590000], rate=19823076.92/min [8600000], rate=19846153.85/min [8610000], rate=19869230.77/min [8620000], rate=19892307.69/min [8630000], rate=19915384.62/min [8640000], rate=19938461.54/min [8650000], rate=19961538.46/min [8660000], rate=19984615.38/min [8670000], rate=20007692.31/min [8680000], rate=20030769.23/min [8690000], rate=20053846.15/min [8700000], rate=20076923.08/min [8710000], rate=20100000.00/min [8720000], rate=20123076.92/min [8730000], rate=20146153.85/min [8740000], rate=20169230.77/min [8750000], rate=20192307.69/min [8760000], rate=20215384.62/min [8770000], rate=20238461.54/min [8780000], rate=20261538.46/min [8790000], rate=20284615.38/min [8800000], rate=20307692.31/min [8810000], rate=20330769.23/min [8820000], rate=20353846.15/min [8830000], rate=20376923.08/min [8840000], rate=19644444.44/min [8850000], rate=19666666.67/min [8860000], rate=19688888.89/min [8870000], rate=19711111.11/min [8880000], rate=19733333.33/min [8890000], rate=19755555.56/min [8900000], rate=19777777.78/min [8910000], rate=19800000.00/min [8920000], rate=19822222.22/min 08:13:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file GM24385_0001_RNA_0001_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -GM24385_0001_RNA_0001_23H5VFLT4_s24.introns: identified 4284 cancer introns 08:13:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file GM24385_0001_RNA_0001_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns.prelim 08:13:26 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/prelim_introns.ok 08:13:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns 08:13:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns 08:13:27 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/introns_filtered.ok 08:13:27 : INFO : -found 1950 cancer introns 08:13:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GM24385_0001_RNA_0001_23H5VFLT4_s24.introns --cancer_introns GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed 08:13:27 : INFO : Creating the BED File. 08:13:33 : INFO : Saving Bed File as GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed 08:13:33 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GM24385_0001_RNA_0001_23H5VFLT4_s24.introns --cancer_introns GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed 08:13:33 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/intron_igv_bed.ok 08:13:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed --bam GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24 [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai 08:27:34 : INFO : Execution Time = 14.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed --bam GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24 08:27:34 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/reads_alignments_extracted.ok 08:27:34 : INFO : Running: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.bam 08:27:35 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.bam 08:27:35 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/sort_cancer_intron_reads.ok 08:27:35 : INFO : Running: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.bam [bam_sort_core] merging from 68 files and 1 in-memory blocks... 08:44:56 : INFO : Execution Time = 17.35 minutes. CMD: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.bam 08:44:56 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/sort_gene_reads.ok 08:44:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr5. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr10. Done with chr chr11. Done with chr chr12. Done with chr chr13. Done with chr chr14. Done with chr chr15. Done with chr chr16. Done with chr chr17. Done with chr chr18. Done with chr chr19. Done with chr chr20. Done with chr chr21. Done with chr chr22. 08:51:19 : INFO : Execution Time = 6.39 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.bam 08:51:19 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp.ok 08:51:19 : INFO : Running: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 8 files and 1 in-memory blocks... 08:53:47 : INFO : Execution Time = 2.47 minutes. CMD: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp 08:53:47 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:53:47 : INFO : Running: samtools index GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam 08:54:05 : INFO : Execution Time = 0.29 minutes. CMD: samtools index GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam 08:54:05 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/GM24385_0001_RNA_0001_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.indexed.ok 08:54:05 : INFO : Running: samtools index GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.sorted.bam 08:54:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools index GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.sorted.bam 08:54:05 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/GM24385_0001_RNA_0001_23H5VFLT4_s24.cancer_intron_reads.sorted.bam.indexed.ok 08:54:05 : INFO : Running: create_report GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output GM24385_0001_RNA_0001_23H5VFLT4_s24.ctat-splicing.igv.html --track-config GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: GM24385_0001_RNA_0001_23H5VFLT4_s24' 09:01:40 : INFO : Execution Time = 7.58 minutes. CMD: create_report GM24385_0001_RNA_0001_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output GM24385_0001_RNA_0001_23H5VFLT4_s24.ctat-splicing.igv.html --track-config GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: GM24385_0001_RNA_0001_23H5VFLT4_s24' 09:01:40 : INFO : Running: touch /tmp/nxf.CBHuMgmDGB/GM24385_0001_RNA_0001_23H5VFLT4_s24.chckpts/igv_create_html.ok 09:01:40 : INFO : done.