CMD: /users/enovoa/imilenkovic/software/miniconda3/envs/isoquant/bin/isoquant.py --reference /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/GRCm39.genome.fa --genedb /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/gencode.vM28.annotation.gtf --complete_genedb --bam /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/HRas_sorted.bam --data_type nanopore -o HRas
2022-05-04 09:29:28,109 - WARNING - HRas/00_HRas_sorted folder already exists, some files may be overwritten
2022-05-04 09:29:28,110 - WARNING - HRas/00_HRas_sorted/aux folder already exists, some files may be overwritten
2022-05-04 09:29:28,116 - INFO -  === IsoQuant pipeline started === 
2022-05-04 09:29:28,119 - INFO - Converting gene annotation file to .db format (takes a while)...
2022-05-04 09:37:16,655 - INFO - Gene database written to /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:37:16,656 - INFO - Provide this database next time to avoid excessive conversion
2022-05-04 09:37:16,668 - INFO - Loading gene database from /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:37:16,686 - INFO - Loading reference genome from /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/GRCm39.genome.fa
2022-05-04 09:37:55,192 - INFO - Processing 1 sample
2022-05-04 09:37:55,193 - INFO - Processing sample 00_HRas_sorted
2022-05-04 09:37:55,193 - INFO - Sample has 1 BAM file: /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/HRas_sorted.bam
2022-05-04 09:37:55,193 - INFO - Assigning reads to isoforms
2022-05-04 09:37:56,615 - INFO - Processing chromosome chr7
2022-05-04 09:37:57,127 - INFO - Processing chromosome chr2
2022-05-04 09:37:57,588 - INFO - Processing chromosome chr1
2022-05-04 09:37:57,879 - INFO - Processing chromosome chr5
2022-05-04 09:37:58,606 - INFO - Processing chromosome chr9
2022-05-04 09:37:58,981 - INFO - Processing chromosome chr6
2022-05-04 09:37:59,190 - INFO - Processing chromosome chr12
2022-05-04 09:37:59,669 - INFO - Processing chromosome chr3
2022-05-04 09:38:00,205 - INFO - Processing chromosome chr11
2022-05-04 09:38:00,710 - INFO - Processing chromosome chr4
2022-05-04 09:38:01,382 - INFO - Processing chromosome chr17
2022-05-04 09:38:01,619 - INFO - Processing chromosome chr8
2022-05-04 09:38:02,245 - INFO - Processing chromosome chr14
2022-05-04 09:38:02,620 - INFO - Processing chromosome chr10
2022-05-04 09:38:03,074 - INFO - Processing chromosome chr13
2022-05-04 09:38:03,976 - INFO - Processing chromosome chrX
2022-05-04 09:41:56,229 - INFO - Finished processing chromosome chrX
2022-05-04 09:41:57,138 - INFO - Processing chromosome chr15
2022-05-04 09:42:04,026 - INFO - Finished processing chromosome chr12
2022-05-04 09:42:05,091 - INFO - Processing chromosome chr16
2022-05-04 09:42:20,592 - INFO - Finished processing chromosome chr14
2022-05-04 09:42:21,085 - INFO - Processing chromosome chr19
2022-05-04 09:42:31,499 - INFO - Finished processing chromosome chr13
2022-05-04 09:42:32,849 - INFO - Processing chromosome chr18
2022-05-04 09:42:45,310 - INFO - Finished processing chromosome chr17
2022-05-04 09:42:46,704 - INFO - Processing chromosome chrY
2022-05-04 09:42:49,760 - INFO - Finished processing chromosome chr8
2022-05-04 09:42:50,047 - INFO - Processing chromosome chrM
2022-05-04 09:43:05,123 - INFO - Finished processing chromosome chr10
2022-05-04 09:43:25,860 - INFO - Finished processing chromosome chr3
2022-05-04 09:43:29,098 - INFO - Finished processing chromosome chr6
2022-05-04 09:43:35,768 - INFO - Finished processing chromosome chr4
2022-05-04 09:43:47,438 - INFO - Finished processing chromosome chrY
2022-05-04 09:44:02,433 - INFO - Finished processing chromosome chrM
2022-05-04 09:44:08,362 - INFO - Finished processing chromosome chr5
2022-05-04 09:44:15,131 - INFO - Finished processing chromosome chr9
2022-05-04 09:44:30,216 - INFO - Finished processing chromosome chr1
2022-05-04 09:44:33,541 - INFO - Finished processing chromosome chr16
2022-05-04 09:44:37,186 - INFO - Finished processing chromosome chr11
2022-05-04 09:44:43,474 - INFO - Finished processing chromosome chr18
2022-05-04 09:44:54,112 - INFO - Finished processing chromosome chr2
2022-05-04 09:44:54,435 - INFO - Finished processing chromosome chr19
2022-05-04 09:45:01,628 - INFO - Finished processing chromosome chr15
2022-05-04 09:45:12,609 - INFO - Finished processing chromosome chr7
2022-05-04 09:45:13,336 - INFO - Resolving multimappers
2022-05-04 09:45:18,725 - INFO - Finishing read assignment, total assignments 727585, polyA percentage 82.1
2022-05-04 09:45:19,103 - INFO - Read assignments files saved to HRas/00_HRas_sorted/aux/00_HRas_sorted.save*. 
2022-05-04 09:45:19,104 - INFO - To keep these intermediate files for debug purposes use --keep_tmp flag
2022-05-04 09:45:19,299 - INFO - Total alignments processed: 727585, polyA tail detected in 597597 (82.1%)
2022-05-04 09:45:19,959 - INFO - Processing assigned reads 00_HRas_sorted
2022-05-04 09:45:20,741 - INFO - Processing chromosome chr7
2022-05-04 09:45:20,746 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr7
2022-05-04 09:45:21,244 - INFO - Processing chromosome chr2
2022-05-04 09:45:21,249 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr2
2022-05-04 09:45:21,741 - INFO - Processing chromosome chr1
2022-05-04 09:45:21,747 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr1
2022-05-04 09:45:22,169 - INFO - Processing chromosome chr5
2022-05-04 09:45:22,173 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr5
2022-05-04 09:45:22,352 - INFO - Processing chromosome chr9
2022-05-04 09:45:22,357 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr9
2022-05-04 09:45:23,332 - INFO - Processing chromosome chr6
2022-05-04 09:45:23,336 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr6
2022-05-04 09:45:23,519 - INFO - Processing chromosome chr12
2022-05-04 09:45:23,541 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr12
2022-05-04 09:45:24,245 - INFO - Processing chromosome chr3
2022-05-04 09:45:24,250 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr3
2022-05-04 09:45:25,315 - INFO - Processing chromosome chr11
2022-05-04 09:45:25,321 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr11
2022-05-04 09:45:26,274 - INFO - Processing chromosome chr4
2022-05-04 09:45:26,279 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr4
2022-05-04 09:45:26,888 - INFO - Processing chromosome chr17
2022-05-04 09:45:26,893 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr17
2022-05-04 09:45:28,318 - INFO - Processing chromosome chr8
2022-05-04 09:45:28,323 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr8
2022-05-04 09:45:28,726 - INFO - Processing chromosome chr14
2022-05-04 09:45:28,731 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr14
2022-05-04 09:45:30,012 - INFO - Processing chromosome chr10
2022-05-04 09:45:30,033 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr10
2022-05-04 09:45:31,401 - INFO - Processing chromosome chr13
2022-05-04 09:45:31,407 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr13
2022-05-04 09:45:33,477 - INFO - Processing chromosome chrX
2022-05-04 09:45:33,483 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chrX
2022-05-04 09:45:42,814 - INFO - Finished processing chromosome chr12
2022-05-04 09:45:44,264 - INFO - Processing chromosome chr15
2022-05-04 09:45:44,269 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr15
2022-05-04 09:45:49,287 - INFO - Finished processing chromosome chr14
2022-05-04 09:45:50,473 - INFO - Processing chromosome chr16
2022-05-04 09:45:50,477 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr16
2022-05-04 09:45:51,503 - INFO - Finished processing chromosome chr6
2022-05-04 09:45:51,990 - INFO - Processing chromosome chr19
2022-05-04 09:45:51,995 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr19
2022-05-04 09:45:54,047 - INFO - Finished processing chromosome chrX
2022-05-04 09:45:54,196 - INFO - Finished processing chromosome chr17
2022-05-04 09:45:55,156 - INFO - Processing chromosome chr18
2022-05-04 09:45:55,159 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chr18
2022-05-04 09:45:55,995 - INFO - Processing chromosome chrY
2022-05-04 09:45:55,999 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chrY
2022-05-04 09:45:56,283 - INFO - Finished processing chromosome chr13
2022-05-04 09:45:56,322 - INFO - Finished processing chromosome chr2
2022-05-04 09:45:56,723 - INFO - Finished processing chromosome chr5
2022-05-04 09:45:57,876 - INFO - Finished processing chromosome chr3
2022-05-04 09:45:57,927 - INFO - Finished processing chromosome chr9
2022-05-04 09:45:58,147 - INFO - Finished processing chromosome chr1
2022-05-04 09:45:58,173 - INFO - Finished processing chromosome chrY
2022-05-04 09:46:00,007 - INFO - Finished processing chromosome chr4
2022-05-04 09:46:00,327 - INFO - Finished processing chromosome chr8
2022-05-04 09:46:00,937 - INFO - Processing chromosome chrM
2022-05-04 09:46:00,943 - INFO - Loading read assignments from HRas/00_HRas_sorted/aux/00_HRas_sorted.save_chrM
2022-05-04 09:46:01,468 - INFO - Finished processing chromosome chr10
2022-05-04 09:46:03,507 - INFO - Finished processing chromosome chr16
2022-05-04 09:46:03,934 - INFO - Finished processing chromosome chr18
2022-05-04 09:46:04,460 - INFO - Finished processing chromosome chr7
2022-05-04 09:46:05,702 - INFO - Finished processing chromosome chr15
2022-05-04 09:46:07,236 - INFO - Finished processing chromosome chr11
2022-05-04 09:46:09,101 - INFO - Finished processing chromosome chr19
2022-05-04 09:46:10,268 - INFO - Finished processing chromosome chrM
2022-05-04 09:46:11,961 - INFO - Scale factor for group NA = 2.18
2022-05-04 09:46:12,152 - INFO - Scale factor for group NA = 2.35
2022-05-04 09:46:12,739 - INFO - Scale factor for group NA = 2.23
2022-05-04 09:46:12,769 - INFO - Gene counts are stored in HRas/00_HRas_sorted/00_HRas_sorted.gene_counts.tsv
2022-05-04 09:46:12,769 - INFO - Transcript counts are stored in HRas/00_HRas_sorted/00_HRas_sorted.transcript_counts.tsv
2022-05-04 09:46:12,769 - INFO - Read assignments are stored in HRas/00_HRas_sorted/00_HRas_sorted.read_assignments.tsv
2022-05-04 09:46:12,770 - INFO - Read assignment statistics
2022-05-04 09:46:12,770 - INFO - ambiguous: 86699
2022-05-04 09:46:12,770 - INFO - inconsistent: 239443
2022-05-04 09:46:12,770 - INFO - noninformative: 18399
2022-05-04 09:46:12,770 - INFO - unique: 327165
2022-05-04 09:46:12,770 - INFO - unique_minor_difference: 55879
2022-05-04 09:46:12,770 - INFO - Transcript model file HRas/00_HRas_sorted/00_HRas_sorted.transcript_models.gtf
2022-05-04 09:46:12,770 - INFO - Transcript model statistics
2022-05-04 09:46:12,770 - INFO - known: 10818
2022-05-04 09:46:12,770 - INFO - novel_in_catalog: 168
2022-05-04 09:46:12,770 - INFO - novel_not_in_catalog: 75
2022-05-04 09:46:13,502 - INFO - Processed sample 00_HRas_sorted
2022-05-04 09:46:13,504 - INFO - Processed 1 sample
2022-05-04 09:46:13,504 - INFO -  === IsoQuant pipeline finished ===