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/3c/ec0f82af30d147b2e71579937949ce/659_6i-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/b4a7c1e7643cc19a189d6e3d8bee0c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/1334352268c0695f37d4ead59565d2/659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/ec0f82af30d147b2e71579937949ce/659_6i-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/b4a7c1e7643cc19a189d6e3d8bee0c/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/ec0f82af30d147b2e71579937949ce/659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 08:12:57 : INFO : -reading 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rate=16000000.00/min [5610000], rate=16028571.43/min [5620000], rate=15327272.73/min [5630000], rate=15354545.45/min [5640000], rate=15381818.18/min [5650000], rate=15409090.91/min [5660000], rate=15436363.64/min [5670000], rate=15463636.36/min [5680000], rate=15490909.09/min [5690000], rate=15518181.82/min [5700000], rate=15545454.55/min [5710000], rate=15572727.27/min [5720000], rate=15600000.00/min [5730000], rate=15627272.73/min [5740000], rate=15654545.45/min [5750000], rate=15681818.18/min [5760000], rate=15709090.91/min [5770000], rate=15736363.64/min [5780000], rate=15763636.36/min [5790000], rate=15790909.09/min [5800000], rate=15818181.82/min [5810000], rate=15845454.55/min [5820000], rate=15872727.27/min [5830000], rate=15900000.00/min [5840000], rate=15927272.73/min [5850000], rate=15954545.45/min [5860000], rate=15981818.18/min [5870000], rate=16009090.91/min [5880000], rate=16036363.64/min [5890000], rate=16063636.36/min [5900000], rate=16090909.09/min [5910000], rate=16118181.82/min [5920000], rate=16145454.55/min [5930000], rate=15469565.22/min [5940000], rate=15495652.17/min [5950000], rate=15521739.13/min [5960000], rate=15547826.09/min [5970000], rate=15573913.04/min [5980000], rate=15600000.00/min [5990000], rate=15626086.96/min [6000000], rate=15652173.91/min [6010000], rate=15678260.87/min [6020000], rate=15704347.83/min [6030000], rate=15730434.78/min [6040000], rate=15756521.74/min [6050000], rate=15782608.70/min [6060000], rate=15808695.65/min [6070000], rate=15834782.61/min [6080000], rate=15860869.57/min [6090000], rate=15886956.52/min [6100000], rate=15913043.48/min [6110000], rate=15939130.43/min [6120000], rate=15965217.39/min [6130000], rate=15991304.35/min [6140000], rate=16017391.30/min [6150000], rate=16043478.26/min [6160000], rate=16069565.22/min [6170000], rate=16095652.17/min [6180000], rate=16121739.13/min [6190000], rate=16147826.09/min [6200000], rate=16173913.04/min [6210000], rate=16200000.00/min [6220000], rate=16226086.96/min [6230000], rate=16252173.91/min [6240000], rate=16278260.87/min [6250000], rate=16304347.83/min [6260000], rate=16330434.78/min [6270000], rate=15675000.00/min [6280000], rate=15700000.00/min [6290000], rate=15725000.00/min [6300000], rate=15750000.00/min [6310000], rate=15775000.00/min [6320000], rate=15800000.00/min [6330000], rate=15825000.00/min [6340000], rate=15850000.00/min [6350000], rate=15875000.00/min [6360000], rate=15900000.00/min [6370000], rate=15925000.00/min [6380000], rate=15950000.00/min [6390000], rate=15975000.00/min [6400000], rate=16000000.00/min [6410000], rate=16025000.00/min [6420000], rate=16050000.00/min [6430000], rate=16075000.00/min [6440000], rate=16100000.00/min [6450000], rate=16125000.00/min [6460000], rate=16150000.00/min [6470000], rate=16175000.00/min [6480000], rate=16200000.00/min [6490000], rate=16225000.00/min [6500000], rate=16250000.00/min [6510000], rate=16275000.00/min [6520000], rate=16300000.00/min [6530000], rate=16325000.00/min [6540000], rate=16350000.00/min [6550000], rate=16375000.00/min [6560000], rate=16400000.00/min [6570000], rate=16425000.00/min [6580000], rate=16450000.00/min [6590000], rate=16475000.00/min [6600000], rate=15840000.00/min [6610000], rate=15864000.00/min [6620000], rate=15888000.00/min [6630000], rate=15912000.00/min [6640000], rate=15936000.00/min [6650000], rate=15960000.00/min [6660000], rate=15984000.00/min [6670000], rate=16008000.00/min [6680000], rate=16032000.00/min [6690000], rate=16056000.00/min [6700000], rate=16080000.00/min [6710000], rate=16104000.00/min [6720000], rate=16128000.00/min [6730000], rate=16152000.00/min [6740000], rate=16176000.00/min [6750000], rate=16200000.00/min [6760000], rate=16224000.00/min [6770000], rate=16248000.00/min [6780000], rate=16272000.00/min [6790000], rate=16296000.00/min [6800000], rate=16320000.00/min [6810000], rate=16344000.00/min [6820000], rate=16368000.00/min [6830000], rate=16392000.00/min [6840000], rate=16416000.00/min [6850000], rate=16440000.00/min [6860000], rate=16464000.00/min [6870000], rate=16488000.00/min [6880000], rate=16512000.00/min [6890000], rate=16536000.00/min [6900000], rate=16560000.00/min [6910000], rate=16584000.00/min [6920000], rate=16608000.00/min [6930000], rate=16632000.00/min [6940000], rate=16656000.00/min [6950000], rate=16038461.54/min [6960000], rate=16061538.46/min [6970000], rate=16084615.38/min [6980000], rate=16107692.31/min [6990000], rate=16130769.23/min [7000000], rate=16153846.15/min [7010000], rate=16176923.08/min [7020000], rate=16200000.00/min [7030000], rate=16223076.92/min [7040000], rate=16246153.85/min [7050000], rate=16269230.77/min [7060000], rate=16292307.69/min [7070000], rate=16315384.62/min [7080000], rate=16338461.54/min [7090000], rate=16361538.46/min [7100000], rate=16384615.38/min [7110000], rate=16407692.31/min [7120000], rate=16430769.23/min [7130000], rate=16453846.15/min [7140000], rate=16476923.08/min [7150000], rate=16500000.00/min [7160000], rate=16523076.92/min [7170000], rate=16546153.85/min [7180000], rate=16569230.77/min [7190000], rate=16592307.69/min [7200000], rate=16615384.62/min [7210000], rate=16638461.54/min [7220000], rate=16661538.46/min [7230000], rate=16684615.38/min [7240000], rate=16707692.31/min [7250000], rate=16730769.23/min [7260000], rate=16753846.15/min [7270000], rate=16155555.56/min [7280000], rate=16177777.78/min [7290000], rate=16200000.00/min [7300000], rate=16222222.22/min [7310000], rate=16244444.44/min [7320000], rate=16266666.67/min [7330000], rate=16288888.89/min [7340000], rate=16311111.11/min [7350000], rate=16333333.33/min [7360000], rate=16355555.56/min [7370000], rate=16377777.78/min [7380000], rate=16400000.00/min [7390000], rate=16422222.22/min [7400000], rate=16444444.44/min [7410000], rate=16466666.67/min [7420000], rate=16488888.89/min [7430000], rate=16511111.11/min [7440000], rate=16533333.33/min [7450000], rate=16555555.56/min [7460000], rate=16577777.78/min [7470000], rate=16600000.00/min 08:13:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_6i-T1-TRNA-1_B23MHV2LT4_1.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. -659_6i-T1-TRNA-1_B23MHV2LT4_1.introns: identified 3859 cancer introns 08:13:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:13:32 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:13:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:13:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:13:32 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:13:32 : INFO : -found 1393 cancer introns 08:13:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:13:33 : INFO : Creating the BED File. 08:13:36 : INFO : Saving Bed File as 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:13:36 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:13:36 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:13:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_6i-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 08:23:22 : INFO : Execution Time = 9.77 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_6i-T1-TRNA-1_B23MHV2LT4_1 08:23:22 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 08:23:22 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 08:23:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 08:23:22 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 08:23:22 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 49 files and 1 in-memory blocks... 08:34:13 : INFO : Execution Time = 10.85 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 08:34:13 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 08:34:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_6i-T1-TRNA-1_B23MHV2LT4_1.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. 08:37:09 : INFO : Execution Time = 2.92 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 08:37:09 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:37:09 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 08:37:42 : INFO : Execution Time = 0.56 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 08:37:42 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:37:42 : INFO : Running: samtools index 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 08:37:46 : INFO : Execution Time = 0.06 minutes. CMD: samtools index 659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 08:37:46 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_6i-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:37:46 : INFO : Running: samtools index 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 08:37:46 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 08:37:46 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_6i-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:37:46 : INFO : Running: create_report 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_6i-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_6i-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_6i-T1-TRNA-1_B23MHV2LT4_1' 08:42:08 : INFO : Execution Time = 4.36 minutes. CMD: create_report 659_6i-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_6i-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_6i-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_6i-T1-TRNA-1_B23MHV2LT4_1' 08:42:08 : INFO : Running: touch /tmp/nxf.5xHbWiOl6x/659_6i-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 08:42:08 : INFO : done.