Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam 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/c9/8da7618251a79ea63fc8d900222f10/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/dfbb32fd89ba107e4305d79a2576c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/27385695e43288cff28ebcd46dc4c9/659_bTo-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/8da7618251a79ea63fc8d900222f10/.command.run ==> STAGING COMPLETE (7 inputs) 09:24:40 : INFO : -reading 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[5790000], rate=14475000.00/min [5800000], rate=14500000.00/min [5810000], rate=14525000.00/min [5820000], rate=14550000.00/min [5830000], rate=14575000.00/min [5840000], rate=14600000.00/min [5850000], rate=14625000.00/min [5860000], rate=14650000.00/min [5870000], rate=14675000.00/min [5880000], rate=14700000.00/min [5890000], rate=14725000.00/min [5900000], rate=14750000.00/min [5910000], rate=14775000.00/min [5920000], rate=14208000.00/min [5930000], rate=14232000.00/min [5940000], rate=14256000.00/min [5950000], rate=14280000.00/min [5960000], rate=14304000.00/min [5970000], rate=14328000.00/min [5980000], rate=14352000.00/min [5990000], rate=14376000.00/min [6000000], rate=14400000.00/min [6010000], rate=14424000.00/min [6020000], rate=14448000.00/min [6030000], rate=14472000.00/min [6040000], rate=14496000.00/min [6050000], rate=14520000.00/min [6060000], rate=14544000.00/min [6070000], rate=14568000.00/min [6080000], rate=14592000.00/min [6090000], rate=14616000.00/min [6100000], rate=14640000.00/min [6110000], rate=14664000.00/min [6120000], rate=14688000.00/min [6130000], rate=14712000.00/min [6140000], rate=14736000.00/min [6150000], rate=14760000.00/min [6160000], rate=14784000.00/min [6170000], rate=14808000.00/min [6180000], rate=14261538.46/min [6190000], rate=14284615.38/min [6200000], rate=14307692.31/min [6210000], rate=14330769.23/min [6220000], rate=14353846.15/min [6230000], rate=14376923.08/min [6240000], rate=14400000.00/min [6250000], rate=14423076.92/min [6260000], rate=14446153.85/min [6270000], rate=14469230.77/min [6280000], rate=14492307.69/min [6290000], rate=14515384.62/min [6300000], rate=14538461.54/min [6310000], rate=14561538.46/min [6320000], rate=14584615.38/min [6330000], rate=14607692.31/min [6340000], rate=14630769.23/min [6350000], rate=14653846.15/min [6360000], rate=14676923.08/min [6370000], rate=14700000.00/min [6380000], rate=14723076.92/min [6390000], rate=14746153.85/min [6400000], rate=14222222.22/min [6410000], rate=14244444.44/min [6420000], rate=14266666.67/min [6430000], rate=14288888.89/min [6440000], rate=14311111.11/min [6450000], rate=14333333.33/min [6460000], rate=14355555.56/min [6470000], rate=14377777.78/min [6480000], rate=14400000.00/min [6490000], rate=14422222.22/min [6500000], rate=14444444.44/min [6510000], rate=14466666.67/min [6520000], rate=14488888.89/min [6530000], rate=14511111.11/min [6540000], rate=14533333.33/min [6550000], rate=14555555.56/min [6560000], rate=14577777.78/min [6570000], rate=14600000.00/min [6580000], rate=14622222.22/min [6590000], rate=14644444.44/min [6600000], rate=14666666.67/min [6610000], rate=14688888.89/min [6620000], rate=14711111.11/min [6630000], rate=14733333.33/min [6640000], rate=14755555.56/min [6650000], rate=14250000.00/min [6660000], rate=14271428.57/min [6670000], rate=14292857.14/min [6680000], rate=14314285.71/min [6690000], rate=14335714.29/min [6700000], rate=14357142.86/min [6710000], rate=14378571.43/min [6720000], rate=14400000.00/min [6730000], rate=14421428.57/min [6740000], rate=14442857.14/min [6750000], rate=14464285.71/min [6760000], rate=14485714.29/min [6770000], rate=14507142.86/min [6780000], rate=14528571.43/min [6790000], rate=14550000.00/min [6800000], rate=14571428.57/min [6810000], rate=14592857.14/min [6820000], rate=14614285.71/min [6830000], rate=14635714.29/min [6840000], rate=14657142.86/min [6850000], rate=14678571.43/min [6860000], rate=14700000.00/min [6870000], rate=14721428.57/min [6880000], rate=14742857.14/min [6890000], rate=14764285.71/min [6900000], rate=14785714.29/min [6910000], rate=14296551.72/min [6920000], rate=14317241.38/min [6930000], rate=14337931.03/min [6940000], rate=14358620.69/min [6950000], rate=14379310.34/min [6960000], rate=14400000.00/min [6970000], rate=14420689.66/min [6980000], rate=14441379.31/min [6990000], rate=14462068.97/min [7000000], rate=14482758.62/min [7010000], rate=14503448.28/min [7020000], rate=14524137.93/min [7030000], rate=14544827.59/min [7040000], rate=14565517.24/min [7050000], rate=14586206.90/min [7060000], rate=14606896.55/min [7070000], rate=14627586.21/min [7080000], rate=14648275.86/min [7090000], rate=14668965.52/min [7100000], rate=14689655.17/min [7110000], rate=14710344.83/min [7120000], rate=14731034.48/min [7130000], rate=14751724.14/min [7140000], rate=14772413.79/min [7150000], rate=14793103.45/min [7160000], rate=14813793.10/min [7170000], rate=14340000.00/min [7180000], rate=14360000.00/min [7190000], rate=14380000.00/min [7200000], rate=14400000.00/min [7210000], rate=14420000.00/min [7220000], rate=14440000.00/min [7230000], rate=14460000.00/min [7240000], rate=14480000.00/min [7250000], rate=14500000.00/min [7260000], rate=14520000.00/min [7270000], rate=14540000.00/min [7280000], rate=14560000.00/min [7290000], rate=14580000.00/min [7300000], rate=14600000.00/min [7310000], rate=14620000.00/min [7320000], rate=14640000.00/min 09:25:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bTo-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_bTo-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7808 cancer introns 09:25:19 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 09:25:19 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 09:25:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 09:25:20 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 09:25:20 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 09:25:20 : INFO : -found 3129 cancer introns 09:25:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:25:20 : INFO : Creating the BED File. 09:25:27 : INFO : Saving Bed File as 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:25:27 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:25:27 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 09:25:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:52:43 : INFO : Execution Time = 27.26 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 09:52:43 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:52:43 : INFO : Running: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:52:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:52:43 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:52:43 : INFO : Running: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 122 files and 1 in-memory blocks... 10:22:58 : INFO : Execution Time = 30.25 minutes. CMD: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 10:22:58 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 10:22:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bTo-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. 10:31:36 : INFO : Execution Time = 8.64 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 10:31:36 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:31:36 : INFO : Running: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:32:27 : INFO : Execution Time = 0.85 minutes. CMD: samtools sort -o 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 10:32:27 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:32:27 : INFO : Running: samtools index 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:32:33 : INFO : Execution Time = 0.09 minutes. CMD: samtools index 659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:32:33 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:32:33 : INFO : Running: samtools index 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:32:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:32:33 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bTo-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:32:33 : INFO : Running: create_report 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bTo-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bTo-T1-TRNA-1_B23MHV2LT4_1' 10:38:47 : INFO : Execution Time = 6.23 minutes. CMD: create_report 659_bTo-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bTo-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bTo-T1-TRNA-1_B23MHV2LT4_1' 10:38:47 : INFO : Running: touch /tmp/nxf.FFGJf5WG6c/659_bTo-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 10:38:47 : INFO : done.