.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/ff8f13b872109cabdbff2580032fca/.command.err
Size: 10.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt
Content

20:12:17 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[350000], rate=21000000.00/min 
[360000], rate=21600000.00/min 
[370000], rate=22200000.00/min 
[380000], rate=22800000.00/min 
[390000], rate=23400000.00/min 
[400000], rate=24000000.00/min 
[410000], rate=24600000.00/min 
[420000], rate=25200000.00/min 
[430000], rate=25800000.00/min 
[440000], rate=26400000.00/min 
[450000], rate=27000000.00/min 
[460000], rate=27600000.00/min 
[470000], rate=28200000.00/min 
[480000], rate=28800000.00/min 
[490000], rate=29400000.00/min 
[500000], rate=30000000.00/min 
[510000], rate=30600000.00/min 
[520000], rate=31200000.00/min 
[530000], rate=31800000.00/min 
[540000], rate=32400000.00/min 
[550000], rate=33000000.00/min 
[560000], rate=33600000.00/min 
[570000], rate=34200000.00/min 
[580000], rate=34800000.00/min 
[590000], rate=35400000.00/min 
[600000], rate=36000000.00/min 
[610000], rate=36600000.00/min 
[620000], rate=37200000.00/min 
[630000], rate=37800000.00/min 
[640000], rate=19200000.00/min 
[650000], rate=19500000.00/min 
[660000], rate=19800000.00/min 
[670000], rate=20100000.00/min 
[680000], rate=20400000.00/min 
[690000], rate=20700000.00/min 
[700000], rate=21000000.00/min 
[710000], rate=21300000.00/min 
[720000], rate=21600000.00/min 
[730000], rate=21900000.00/min 
[740000], rate=22200000.00/min 
[750000], rate=22500000.00/min 
[760000], rate=22800000.00/min 
[770000], rate=23100000.00/min 
[780000], rate=23400000.00/min 
[790000], rate=23700000.00/min 
[800000], rate=24000000.00/min 
[810000], rate=24300000.00/min 
[820000], rate=24600000.00/min 
[830000], rate=24900000.00/min 
[840000], rate=25200000.00/min 
[850000], rate=25500000.00/min 
[860000], rate=25800000.00/min 
[870000], rate=26100000.00/min 
[880000], rate=26400000.00/min 
[890000], rate=26700000.00/min 
[900000], rate=27000000.00/min 
[910000], rate=27300000.00/min 
[920000], rate=27600000.00/min 
[930000], rate=27900000.00/min 
[940000], rate=28200000.00/min 
[950000], rate=28500000.00/min 
[960000], rate=28800000.00/min 
[970000], rate=29100000.00/min 
[980000], rate=29400000.00/min 
[990000], rate=29700000.00/min 
[1000000], rate=30000000.00/min 
[1010000], rate=30300000.00/min 
[1020000], rate=30600000.00/min 
[1030000], rate=30900000.00/min 
[1040000], rate=20800000.00/min 
[1050000], rate=21000000.00/min 
[1060000], rate=21200000.00/min 
[1070000], rate=21400000.00/min 
[1080000], rate=21600000.00/min 
[1090000], rate=21800000.00/min 
[1100000], rate=22000000.00/min 
[1110000], rate=22200000.00/min 
[1120000], rate=22400000.00/min 
[1130000], rate=22600000.00/min 
[1140000], rate=22800000.00/min 
[1150000], rate=23000000.00/min 
[1160000], rate=23200000.00/min 
[1170000], rate=23400000.00/min 
[1180000], rate=23600000.00/min 
[1190000], rate=23800000.00/min 
[1200000], rate=24000000.00/min 
[1210000], rate=24200000.00/min 
[1220000], rate=24400000.00/min 
[1230000], rate=24600000.00/min 
[1240000], rate=24800000.00/min 
[1250000], rate=25000000.00/min 20:12:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_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.
-SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns: identified 71 cancer introns
20:12:25 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 
20:12:25 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
20:12:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 
20:12:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 
20:12:26 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
20:12:26 : INFO : -found 31 cancer introns
20:12:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
20:12:26 : INFO :  Creating the BED File.
20:12:27 : INFO : Saving Bed File as SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
20:12:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
20:12:27 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
20:12:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1 
[W::hts_idx_load3] The index file is older than the data file: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
20:12:28 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1 
20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
20:12:28 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
20:12:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
20:12:28 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
20:12:28 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
20:12:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
20:12:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:12:29 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:12:29 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:12:29 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:12:29 : INFO : Running: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1' 
20:12:34 : INFO : Execution Time = 0.08 minutes. CMD: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1' 
20:12:34 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
20:12:34 : INFO : done.