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/d8/4a65ceb8438435e0339e8c688960be/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/5116b92af65cead81bc153a7f4d82b/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/4a65ceb8438435e0339e8c688960be/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 21:35:13 : 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rate=10270588.24/min [8740000], rate=10282352.94/min [8750000], rate=10294117.65/min [8760000], rate=10305882.35/min [8770000], rate=10317647.06/min [8780000], rate=10329411.76/min [8790000], rate=10341176.47/min [8800000], rate=10352941.18/min [8810000], rate=10364705.88/min [8820000], rate=10176923.08/min [8830000], rate=10188461.54/min [8840000], rate=10200000.00/min [8850000], rate=10211538.46/min [8860000], rate=10223076.92/min [8870000], rate=10234615.38/min [8880000], rate=10246153.85/min [8890000], rate=10257692.31/min [8900000], rate=10269230.77/min [8910000], rate=10280769.23/min [8920000], rate=10292307.69/min [8930000], rate=10303846.15/min [8940000], rate=10315384.62/min [8950000], rate=10326923.08/min [8960000], rate=10338461.54/min [8970000], rate=10350000.00/min [8980000], rate=10361538.46/min [8990000], rate=10373076.92/min [9000000], rate=10384615.38/min [9010000], rate=10396153.85/min [9020000], rate=10407692.31/min [9030000], rate=10419230.77/min [9040000], rate=10430769.23/min [9050000], rate=10245283.02/min [9060000], rate=10256603.77/min [9070000], rate=10267924.53/min [9080000], rate=10279245.28/min [9090000], rate=10290566.04/min [9100000], rate=10301886.79/min [9110000], rate=10313207.55/min [9120000], rate=10324528.30/min [9130000], rate=10335849.06/min [9140000], rate=10347169.81/min [9150000], rate=10358490.57/min [9160000], rate=10369811.32/min [9170000], rate=10381132.08/min [9180000], rate=10392452.83/min [9190000], rate=10403773.58/min [9200000], rate=10415094.34/min [9210000], rate=10426415.09/min [9220000], rate=10437735.85/min [9230000], rate=10449056.60/min [9240000], rate=10460377.36/min [9250000], rate=10471698.11/min [9260000], rate=10483018.87/min [9270000], rate=10494339.62/min [9280000], rate=10505660.38/min [9290000], rate=10322222.22/min [9300000], rate=10333333.33/min [9310000], rate=10344444.44/min [9320000], rate=10355555.56/min [9330000], rate=10366666.67/min [9340000], rate=10377777.78/min [9350000], rate=10388888.89/min [9360000], rate=10400000.00/min [9370000], rate=10411111.11/min [9380000], rate=10422222.22/min [9390000], rate=10433333.33/min [9400000], rate=10444444.44/min [9410000], rate=10455555.56/min [9420000], rate=10466666.67/min [9430000], rate=10477777.78/min 21:36:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.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. -FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns: identified 6167 cancer introns 21:36:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim 21:36:21 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok 21:36:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns 21:36:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns 21:36:22 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok 21:36:22 : INFO : -found 2885 cancer introns 21:36:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 21:36:22 : INFO : Creating the BED File. 21:36:32 : INFO : Saving Bed File as FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 21:36:32 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 21:36:32 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok 21:36:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2 [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai 21:57:42 : INFO : Execution Time = 21.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2 21:57:42 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok 21:57:42 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 21:57:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 21:57:43 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok 21:57:43 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.bam