CMD: /users/enovoa/imilenkovic/software/miniconda3/envs/isoquant/bin/isoquant.py --reference /users/enovoa/imilenkovic/references/GRCh38.primary_assembly.genome.fa --genedb /users/enovoa/imilenkovic/references/gencode.v39.annotation.gtf --complete_genedb --bam /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_human_genome_no_discovery/bambu/SK1_sorted.bam --data_type nanopore -o SK1
2022-05-04 00:35:57,974 - WARNING - SK1/00_SK1_sorted folder already exists, some files may be overwritten
2022-05-04 00:35:57,975 - WARNING - SK1/00_SK1_sorted/aux folder already exists, some files may be overwritten
2022-05-04 00:35:57,977 - INFO -  === IsoQuant pipeline started === 
2022-05-04 00:35:57,978 - INFO - Converting gene annotation file to .db format (takes a while)...
2022-05-04 00:47:06,671 - INFO - Gene database written to /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/SK1/gencode.v39.annotation.db
2022-05-04 00:47:06,672 - INFO - Provide this database next time to avoid excessive conversion
2022-05-04 00:47:06,677 - INFO - Loading gene database from /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/SK1/gencode.v39.annotation.db
2022-05-04 00:47:06,692 - INFO - Loading reference genome from /users/enovoa/imilenkovic/references/GRCh38.primary_assembly.genome.fa
2022-05-04 00:47:40,535 - INFO - Processing 1 sample
2022-05-04 00:47:40,535 - INFO - Processing sample 00_SK1_sorted
2022-05-04 00:47:40,535 - INFO - Sample has 1 BAM file: /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_human_genome_no_discovery/bambu/SK1_sorted.bam
2022-05-04 00:47:40,536 - INFO - Assigning reads to isoforms
2022-05-04 00:47:41,632 - INFO - Processing chromosome chr19
2022-05-04 00:47:41,909 - INFO - Processing chromosome chr1
2022-05-04 00:47:41,959 - INFO - Processing chromosome chr17
2022-05-04 00:47:44,152 - INFO - Processing chromosome chr2
2022-05-04 00:47:44,377 - INFO - Processing chromosome chr11
2022-05-04 00:47:45,186 - INFO - Processing chromosome chr12
2022-05-04 00:47:45,489 - INFO - Processing chromosome chr16
2022-05-04 00:47:49,710 - INFO - Processing chromosome chr3
2022-05-04 00:47:51,729 - INFO - Processing chromosome chr7
2022-05-04 00:47:52,434 - INFO - Processing chromosome chr14
2022-05-04 00:47:57,198 - INFO - Processing chromosome chr6
2022-05-04 00:47:58,116 - INFO - Processing chromosome chr15
2022-05-04 00:48:04,548 - INFO - Processing chromosome chr5
2022-05-04 00:48:06,646 - INFO - Processing chromosome chr10
2022-05-04 00:48:11,370 - INFO - Processing chromosome chr8
2022-05-04 00:48:17,946 - INFO - Processing chromosome chr4
2022-05-04 01:08:42,667 - INFO - Finished processing chromosome chr4
2022-05-04 01:08:52,658 - INFO - Processing chromosome chr9
2022-05-04 01:11:36,438 - INFO - Finished processing chromosome chr14
2022-05-04 01:11:47,008 - INFO - Processing chromosome chrX
2022-05-04 01:14:52,587 - INFO - Finished processing chromosome chr16
2022-05-04 01:14:58,098 - INFO - Processing chromosome chr22
2022-05-04 01:15:22,205 - INFO - Finished processing chromosome chr7
2022-05-04 01:15:27,870 - INFO - Processing chromosome chr20
2022-05-04 01:15:33,228 - INFO - Finished processing chromosome chr8
2022-05-04 01:15:47,375 - INFO - Processing chromosome chr13
2022-05-04 01:15:53,516 - INFO - Finished processing chromosome chr10
2022-05-04 01:16:00,803 - INFO - Processing chromosome chr18
2022-05-04 01:24:06,919 - INFO - Finished processing chromosome chr6
2022-05-04 01:24:20,635 - INFO - Processing chromosome chr21
2022-05-04 01:24:24,439 - INFO - Finished processing chromosome chr18
2022-05-04 01:24:32,304 - INFO - Processing chromosome chrY
2022-05-04 01:24:58,942 - INFO - Finished processing chromosome chr17
2022-05-04 01:25:03,105 - INFO - Processing chromosome chrM
2022-05-04 01:25:11,686 - INFO - Finished processing chromosome chrY
2022-05-04 01:27:25,724 - INFO - Finished processing chromosome chr15
2022-05-04 01:27:50,157 - INFO - Finished processing chromosome chr22
2022-05-04 01:28:14,232 - INFO - Finished processing chromosome chr13
2022-05-04 01:28:28,596 - INFO - Finished processing chromosome chr5
2022-05-04 01:29:08,183 - INFO - Finished processing chromosome chr9
2022-05-04 01:29:31,351 - INFO - Finished processing chromosome chr3
2022-05-04 01:29:37,061 - INFO - Finished processing chromosome chrX
2022-05-04 01:29:49,620 - INFO - Finished processing chromosome chr21
2022-05-04 01:30:04,373 - INFO - Finished processing chromosome chr19
2022-05-04 01:31:01,468 - INFO - Finished processing chromosome chrM
2022-05-04 01:31:09,620 - INFO - Finished processing chromosome chr20
2022-05-04 01:31:21,655 - INFO - Finished processing chromosome chr12
2022-05-04 01:32:03,870 - INFO - Finished processing chromosome chr11
2022-05-04 01:32:39,714 - INFO - Finished processing chromosome chr2
2022-05-04 01:33:32,900 - INFO - Finished processing chromosome chr1
2022-05-04 01:33:34,345 - INFO - Resolving multimappers
2022-05-04 01:33:43,569 - INFO - Finishing read assignment, total assignments 1133057, polyA percentage 81.1
2022-05-04 01:33:44,284 - INFO - Read assignments files saved to SK1/00_SK1_sorted/aux/00_SK1_sorted.save*. 
2022-05-04 01:33:44,285 - INFO - To keep these intermediate files for debug purposes use --keep_tmp flag
2022-05-04 01:33:44,769 - INFO - Total alignments processed: 1133057, polyA tail detected in 918816 (81.1%)
2022-05-04 01:33:45,238 - INFO - Processing assigned reads 00_SK1_sorted
2022-05-04 01:33:46,688 - INFO - Processing chromosome chr19
2022-05-04 01:33:46,693 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr19
2022-05-04 01:33:47,313 - INFO - Processing chromosome chr17
2022-05-04 01:33:47,318 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr17
2022-05-04 01:33:47,341 - INFO - Processing chromosome chr1
2022-05-04 01:33:47,346 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr1
2022-05-04 01:33:51,951 - INFO - Processing chromosome chr2
2022-05-04 01:33:51,956 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr2
2022-05-04 01:33:52,396 - INFO - Processing chromosome chr11
2022-05-04 01:33:52,405 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr11
2022-05-04 01:33:54,797 - INFO - Processing chromosome chr12
2022-05-04 01:33:54,805 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr12
2022-05-04 01:33:55,201 - INFO - Processing chromosome chr16
2022-05-04 01:33:55,206 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr16
2022-05-04 01:34:00,970 - INFO - Processing chromosome chr3
2022-05-04 01:34:00,982 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr3
2022-05-04 01:34:03,717 - INFO - Processing chromosome chr7
2022-05-04 01:34:03,726 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr7
2022-05-04 01:34:04,482 - INFO - Processing chromosome chr14
2022-05-04 01:34:04,488 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr14
2022-05-04 01:34:12,456 - INFO - Processing chromosome chr6
2022-05-04 01:34:12,468 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr6
2022-05-04 01:34:12,615 - INFO - Processing chromosome chr15
2022-05-04 01:34:12,621 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr15
2022-05-04 01:34:21,316 - INFO - Processing chromosome chr5
2022-05-04 01:34:21,328 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr5
2022-05-04 01:34:22,956 - INFO - Processing chromosome chr10
2022-05-04 01:34:22,971 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr10
2022-05-04 01:34:28,595 - INFO - Processing chromosome chr8
2022-05-04 01:34:28,611 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr8
2022-05-04 01:34:35,605 - INFO - Processing chromosome chr4
2022-05-04 01:34:35,619 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr4
2022-05-04 01:36:38,191 - INFO - Finished processing chromosome chr14
2022-05-04 01:36:41,347 - INFO - Finished processing chromosome chr4
2022-05-04 01:36:46,771 - INFO - Processing chromosome chr9
2022-05-04 01:36:46,776 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr9
2022-05-04 01:36:53,209 - INFO - Processing chromosome chrX
2022-05-04 01:36:53,214 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chrX
2022-05-04 01:37:10,811 - INFO - Finished processing chromosome chr7
2022-05-04 01:37:14,543 - INFO - Processing chromosome chr22
2022-05-04 01:37:14,549 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr22
2022-05-04 01:37:19,599 - INFO - Finished processing chromosome chr8
2022-05-04 01:37:24,385 - INFO - Finished processing chromosome chr16
2022-05-04 01:37:24,517 - INFO - Processing chromosome chr20
2022-05-04 01:37:24,529 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr20
2022-05-04 01:37:30,955 - INFO - Processing chromosome chr13
2022-05-04 01:37:30,967 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr13
2022-05-04 01:37:49,471 - INFO - Finished processing chromosome chr10
2022-05-04 01:37:54,064 - INFO - Processing chromosome chr18
2022-05-04 01:37:54,073 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr18
2022-05-04 01:38:19,307 - INFO - Finished processing chromosome chr15
2022-05-04 01:38:20,263 - INFO - Finished processing chromosome chr6
2022-05-04 01:38:22,568 - INFO - Processing chromosome chr21
2022-05-04 01:38:22,580 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chr21
2022-05-04 01:38:24,131 - INFO - Processing chromosome chrY
2022-05-04 01:38:24,144 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chrY
2022-05-04 01:38:26,983 - INFO - Finished processing chromosome chrY
2022-05-04 01:38:30,095 - INFO - Finished processing chromosome chr3
2022-05-04 01:38:33,471 - INFO - Finished processing chromosome chr17
2022-05-04 01:38:46,667 - INFO - Finished processing chromosome chr18
2022-05-04 01:38:48,691 - INFO - Finished processing chromosome chr13
2022-05-04 01:38:52,687 - INFO - Processing chromosome chrM
2022-05-04 01:38:52,692 - INFO - Loading read assignments from SK1/00_SK1_sorted/aux/00_SK1_sorted.save_chrM
2022-05-04 01:39:00,391 - INFO - Finished processing chromosome chrX
2022-05-04 01:39:00,427 - INFO - Finished processing chromosome chr22
2022-05-04 01:39:01,255 - INFO - Finished processing chromosome chr21
2022-05-04 01:39:03,815 - INFO - Finished processing chromosome chr5
2022-05-04 01:39:10,951 - INFO - Finished processing chromosome chr2
2022-05-04 01:39:19,371 - INFO - Finished processing chromosome chr9
2022-05-04 01:39:24,427 - INFO - Finished processing chromosome chr11
2022-05-04 01:39:25,907 - INFO - Finished processing chromosome chr12
2022-05-04 01:39:28,894 - INFO - Finished processing chromosome chr20
2022-05-04 01:39:30,065 - INFO - Finished processing chromosome chr19
2022-05-04 01:39:33,108 - INFO - Finished processing chromosome chrM
2022-05-04 01:39:34,029 - INFO - Finished processing chromosome chr1
2022-05-04 01:39:37,214 - INFO - Scale factor for group NA = 1.39
2022-05-04 01:39:37,579 - INFO - Scale factor for group NA = 1.54
2022-05-04 01:39:38,533 - INFO - Scale factor for group NA = 1.42
2022-05-04 01:39:38,606 - INFO - Gene counts are stored in SK1/00_SK1_sorted/00_SK1_sorted.gene_counts.tsv
2022-05-04 01:39:38,606 - INFO - Transcript counts are stored in SK1/00_SK1_sorted/00_SK1_sorted.transcript_counts.tsv
2022-05-04 01:39:38,606 - INFO - Read assignments are stored in SK1/00_SK1_sorted/00_SK1_sorted.read_assignments.tsv
2022-05-04 01:39:38,606 - INFO - Read assignment statistics
2022-05-04 01:39:38,607 - INFO - ambiguous: 205406
2022-05-04 01:39:38,607 - INFO - inconsistent: 370728
2022-05-04 01:39:38,607 - INFO - noninformative: 28289
2022-05-04 01:39:38,608 - INFO - unique: 439752
2022-05-04 01:39:38,608 - INFO - unique_minor_difference: 88882
2022-05-04 01:39:38,608 - INFO - Transcript model file SK1/00_SK1_sorted/00_SK1_sorted.transcript_models.gtf
2022-05-04 01:39:38,608 - INFO - Transcript model statistics
2022-05-04 01:39:38,609 - INFO - known: 15513
2022-05-04 01:39:38,609 - INFO - novel_in_catalog: 501
2022-05-04 01:39:38,609 - INFO - novel_not_in_catalog: 169
2022-05-04 01:39:39,661 - INFO - Processed sample 00_SK1_sorted
2022-05-04 01:39:39,661 - INFO - Processed 1 sample
2022-05-04 01:39:39,661 - INFO -  === IsoQuant pipeline finished ===