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/PMK2_sorted.bam --data_type nanopore -o PMK2
2022-05-04 09:54:33,567 - WARNING - PMK2/00_PMK2_sorted folder already exists, some files may be overwritten
2022-05-04 09:54:33,568 - WARNING - PMK2/00_PMK2_sorted/aux folder already exists, some files may be overwritten
2022-05-04 09:54:33,570 - INFO -  === IsoQuant pipeline started === 
2022-05-04 09:54:33,572 - INFO - Gene annotation file found. Using /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:54:33,572 - INFO - Loading gene database from /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:54:33,589 - 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 09:55:04,046 - INFO - Processing 1 sample
2022-05-04 09:55:04,047 - INFO - Processing sample 00_PMK2_sorted
2022-05-04 09:55:04,047 - INFO - Sample has 1 BAM file: /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/PMK2_sorted.bam
2022-05-04 09:55:04,047 - INFO - Assigning reads to isoforms
2022-05-04 09:55:05,295 - INFO - Processing chromosome chr7
2022-05-04 09:55:05,783 - INFO - Processing chromosome chr2
2022-05-04 09:55:06,274 - INFO - Processing chromosome chr1
2022-05-04 09:55:06,543 - INFO - Processing chromosome chr5
2022-05-04 09:55:06,888 - INFO - Processing chromosome chr9
2022-05-04 09:55:07,233 - INFO - Processing chromosome chr6
2022-05-04 09:55:07,566 - INFO - Processing chromosome chr12
2022-05-04 09:55:07,988 - INFO - Processing chromosome chr3
2022-05-04 09:55:08,231 - INFO - Processing chromosome chr11
2022-05-04 09:55:09,117 - INFO - Processing chromosome chr4
2022-05-04 09:55:09,197 - INFO - Processing chromosome chr17
2022-05-04 09:55:10,209 - INFO - Processing chromosome chr8
2022-05-04 09:55:10,695 - INFO - Processing chromosome chr14
2022-05-04 09:55:11,083 - INFO - Processing chromosome chr10
2022-05-04 09:55:12,009 - INFO - Processing chromosome chr13
2022-05-04 09:55:12,943 - INFO - Processing chromosome chrX
2022-05-04 09:59:02,267 - INFO - Finished processing chromosome chrX
2022-05-04 09:59:03,322 - INFO - Processing chromosome chr15
2022-05-04 09:59:07,750 - INFO - Finished processing chromosome chr12
2022-05-04 09:59:08,501 - INFO - Processing chromosome chr16
2022-05-04 09:59:24,587 - INFO - Finished processing chromosome chr13
2022-05-04 09:59:25,784 - INFO - Processing chromosome chr19
2022-05-04 09:59:27,719 - INFO - Finished processing chromosome chr14
2022-05-04 09:59:28,360 - INFO - Processing chromosome chr18
2022-05-04 09:59:49,699 - INFO - Finished processing chromosome chr17
2022-05-04 09:59:50,562 - INFO - Processing chromosome chrY
2022-05-04 10:00:05,009 - INFO - Finished processing chromosome chr8
2022-05-04 10:00:05,379 - INFO - Processing chromosome chrM
2022-05-04 10:00:19,821 - INFO - Finished processing chromosome chr10
2022-05-04 10:00:39,272 - INFO - Finished processing chromosome chr3
2022-05-04 10:00:49,102 - INFO - Finished processing chromosome chr6
2022-05-04 10:00:50,650 - INFO - Finished processing chromosome chrM
2022-05-04 10:00:54,055 - INFO - Finished processing chromosome chrY
2022-05-04 10:00:56,564 - INFO - Finished processing chromosome chr4
2022-05-04 10:01:32,876 - INFO - Finished processing chromosome chr5
2022-05-04 10:01:45,784 - INFO - Finished processing chromosome chr9
2022-05-04 10:01:46,358 - INFO - Finished processing chromosome chr16
2022-05-04 10:01:47,618 - INFO - Finished processing chromosome chr1
2022-05-04 10:01:56,567 - INFO - Finished processing chromosome chr18
2022-05-04 10:01:56,892 - INFO - Finished processing chromosome chr11
2022-05-04 10:02:01,126 - INFO - Finished processing chromosome chr19
2022-05-04 10:02:05,275 - INFO - Finished processing chromosome chr2
2022-05-04 10:02:14,904 - INFO - Finished processing chromosome chr15
2022-05-04 10:02:26,866 - INFO - Finished processing chromosome chr7
2022-05-04 10:02:27,679 - INFO - Resolving multimappers
2022-05-04 10:02:32,367 - INFO - Finishing read assignment, total assignments 767354, polyA percentage 81.1
2022-05-04 10:02:32,762 - INFO - Read assignments files saved to PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save*. 
2022-05-04 10:02:32,762 - INFO - To keep these intermediate files for debug purposes use --keep_tmp flag
2022-05-04 10:02:32,919 - INFO - Total alignments processed: 767354, polyA tail detected in 622651 (81.1%)
2022-05-04 10:02:33,699 - INFO - Processing assigned reads 00_PMK2_sorted
2022-05-04 10:02:34,538 - INFO - Processing chromosome chr7
2022-05-04 10:02:34,544 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr7
2022-05-04 10:02:35,097 - INFO - Processing chromosome chr2
2022-05-04 10:02:35,103 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr2
2022-05-04 10:02:35,635 - INFO - Processing chromosome chr1
2022-05-04 10:02:35,639 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr1
2022-05-04 10:02:36,146 - INFO - Processing chromosome chr5
2022-05-04 10:02:36,150 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr5
2022-05-04 10:02:36,519 - INFO - Processing chromosome chr9
2022-05-04 10:02:36,524 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr9
2022-05-04 10:02:37,272 - INFO - Processing chromosome chr6
2022-05-04 10:02:37,276 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr6
2022-05-04 10:02:37,561 - INFO - Processing chromosome chr12
2022-05-04 10:02:37,565 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr12
2022-05-04 10:02:38,585 - INFO - Processing chromosome chr3
2022-05-04 10:02:38,590 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr3
2022-05-04 10:02:39,617 - INFO - Processing chromosome chr11
2022-05-04 10:02:39,622 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr11
2022-05-04 10:02:40,841 - INFO - Processing chromosome chr4
2022-05-04 10:02:40,845 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr4
2022-05-04 10:02:41,418 - INFO - Processing chromosome chr17
2022-05-04 10:02:41,422 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr17
2022-05-04 10:02:43,606 - INFO - Processing chromosome chr8
2022-05-04 10:02:43,611 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr8
2022-05-04 10:02:45,412 - INFO - Processing chromosome chr14
2022-05-04 10:02:45,417 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr14
2022-05-04 10:02:48,089 - INFO - Processing chromosome chr10
2022-05-04 10:02:48,093 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr10
2022-05-04 10:02:48,473 - INFO - Processing chromosome chr13
2022-05-04 10:02:48,476 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr13
2022-05-04 10:02:48,647 - INFO - Finished processing chromosome chr12
2022-05-04 10:02:51,304 - INFO - Processing chromosome chrX
2022-05-04 10:02:51,309 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chrX
2022-05-04 10:02:51,743 - INFO - Processing chromosome chr15
2022-05-04 10:02:51,747 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr15
2022-05-04 10:02:58,967 - INFO - Finished processing chromosome chr6
2022-05-04 10:03:00,280 - INFO - Processing chromosome chr16
2022-05-04 10:03:00,287 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr16
2022-05-04 10:03:05,328 - INFO - Finished processing chromosome chr1
2022-05-04 10:03:05,453 - INFO - Finished processing chromosome chr2
2022-05-04 10:03:06,194 - INFO - Processing chromosome chr19
2022-05-04 10:03:06,198 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr19
2022-05-04 10:03:07,151 - INFO - Processing chromosome chr18
2022-05-04 10:03:07,155 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chr18
2022-05-04 10:03:10,255 - INFO - Finished processing chromosome chr5
2022-05-04 10:03:11,274 - INFO - Finished processing chromosome chrX
2022-05-04 10:03:11,362 - INFO - Processing chromosome chrY
2022-05-04 10:03:11,367 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chrY
2022-05-04 10:03:11,529 - INFO - Finished processing chromosome chr13
2022-05-04 10:03:12,081 - INFO - Finished processing chromosome chr7
2022-05-04 10:03:12,657 - INFO - Finished processing chromosome chrY
2022-05-04 10:03:12,748 - INFO - Processing chromosome chrM
2022-05-04 10:03:12,752 - INFO - Loading read assignments from PMK2/00_PMK2_sorted/aux/00_PMK2_sorted.save_chrM
2022-05-04 10:03:12,921 - INFO - Finished processing chromosome chr14
2022-05-04 10:03:15,739 - INFO - Finished processing chromosome chr17
2022-05-04 10:03:16,717 - INFO - Finished processing chromosome chr16
2022-05-04 10:03:17,147 - INFO - Finished processing chromosome chr10
2022-05-04 10:03:18,302 - INFO - Finished processing chromosome chr8
2022-05-04 10:03:20,262 - INFO - Finished processing chromosome chr3
2022-05-04 10:03:20,382 - INFO - Finished processing chromosome chr4
2022-05-04 10:03:20,722 - INFO - Finished processing chromosome chr18
2022-05-04 10:03:21,367 - INFO - Finished processing chromosome chr15
2022-05-04 10:03:21,439 - INFO - Finished processing chromosome chrM
2022-05-04 10:03:21,566 - INFO - Finished processing chromosome chr9
2022-05-04 10:03:22,742 - INFO - Finished processing chromosome chr19
2022-05-04 10:03:26,337 - INFO - Finished processing chromosome chr11
2022-05-04 10:03:28,434 - INFO - Scale factor for group NA = 2.06
2022-05-04 10:03:28,645 - INFO - Scale factor for group NA = 2.21
2022-05-04 10:03:29,447 - INFO - Scale factor for group NA = 2.07
2022-05-04 10:03:29,485 - INFO - Gene counts are stored in PMK2/00_PMK2_sorted/00_PMK2_sorted.gene_counts.tsv
2022-05-04 10:03:29,485 - INFO - Transcript counts are stored in PMK2/00_PMK2_sorted/00_PMK2_sorted.transcript_counts.tsv
2022-05-04 10:03:29,485 - INFO - Read assignments are stored in PMK2/00_PMK2_sorted/00_PMK2_sorted.read_assignments.tsv
2022-05-04 10:03:29,485 - INFO - Read assignment statistics
2022-05-04 10:03:29,485 - INFO - ambiguous: 87268
2022-05-04 10:03:29,485 - INFO - inconsistent: 255066
2022-05-04 10:03:29,485 - INFO - noninformative: 15076
2022-05-04 10:03:29,485 - INFO - unique: 341824
2022-05-04 10:03:29,485 - INFO - unique_minor_difference: 68120
2022-05-04 10:03:29,485 - INFO - Transcript model file PMK2/00_PMK2_sorted/00_PMK2_sorted.transcript_models.gtf
2022-05-04 10:03:29,485 - INFO - Transcript model statistics
2022-05-04 10:03:29,485 - INFO - known: 11461
2022-05-04 10:03:29,486 - INFO - novel_in_catalog: 213
2022-05-04 10:03:29,486 - INFO - novel_not_in_catalog: 101
2022-05-04 10:03:30,325 - INFO - Processed sample 00_PMK2_sorted
2022-05-04 10:03:30,325 - INFO - Processed 1 sample
2022-05-04 10:03:30,325 - INFO -  === IsoQuant pipeline finished ===