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/PMK1_sorted.bam --data_type nanopore -o PMK1
2022-05-04 09:46:16,726 - WARNING - PMK1/00_PMK1_sorted folder already exists, some files may be overwritten
2022-05-04 09:46:16,727 - WARNING - PMK1/00_PMK1_sorted/aux folder already exists, some files may be overwritten
2022-05-04 09:46:16,730 - INFO -  === IsoQuant pipeline started === 
2022-05-04 09:46:16,732 - INFO - Gene annotation file found. Using /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:46:16,732 - INFO - Loading gene database from /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/HRas/gencode.vM28.annotation.db
2022-05-04 09:46:16,747 - 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 09:46:45,908 - INFO - Processing 1 sample
2022-05-04 09:46:45,909 - INFO - Processing sample 00_PMK1_sorted
2022-05-04 09:46:45,909 - INFO - Sample has 1 BAM file: /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_transcriptome_with_discovery/bambu_analysis/PMK1_sorted.bam
2022-05-04 09:46:45,909 - INFO - Assigning reads to isoforms
2022-05-04 09:46:47,204 - INFO - Processing chromosome chr7
2022-05-04 09:46:47,673 - INFO - Processing chromosome chr2
2022-05-04 09:46:48,157 - INFO - Processing chromosome chr1
2022-05-04 09:46:48,456 - INFO - Processing chromosome chr5
2022-05-04 09:46:48,722 - INFO - Processing chromosome chr9
2022-05-04 09:46:49,169 - INFO - Processing chromosome chr6
2022-05-04 09:46:49,459 - INFO - Processing chromosome chr12
2022-05-04 09:46:49,892 - INFO - Processing chromosome chr3
2022-05-04 09:46:50,996 - INFO - Processing chromosome chr4
2022-05-04 09:46:51,005 - INFO - Processing chromosome chr11
2022-05-04 09:46:51,263 - INFO - Processing chromosome chr17
2022-05-04 09:46:51,747 - INFO - Processing chromosome chr8
2022-05-04 09:46:52,338 - INFO - Processing chromosome chr14
2022-05-04 09:46:52,963 - INFO - Processing chromosome chr10
2022-05-04 09:46:53,211 - INFO - Processing chromosome chr13
2022-05-04 09:46:54,186 - INFO - Processing chromosome chrX
2022-05-04 09:50:44,633 - INFO - Finished processing chromosome chrX
2022-05-04 09:50:44,701 - INFO - Finished processing chromosome chr12
2022-05-04 09:50:45,957 - INFO - Processing chromosome chr15
2022-05-04 09:50:46,560 - INFO - Processing chromosome chr16
2022-05-04 09:50:51,367 - INFO - Finished processing chromosome chr14
2022-05-04 09:50:51,791 - INFO - Processing chromosome chr19
2022-05-04 09:50:56,608 - INFO - Finished processing chromosome chr13
2022-05-04 09:50:57,376 - INFO - Processing chromosome chr18
2022-05-04 09:51:13,327 - INFO - Finished processing chromosome chr17
2022-05-04 09:51:14,211 - INFO - Processing chromosome chrY
2022-05-04 09:51:24,867 - INFO - Finished processing chromosome chr8
2022-05-04 09:51:25,194 - INFO - Processing chromosome chrM
2022-05-04 09:51:33,920 - INFO - Finished processing chromosome chr10
2022-05-04 09:51:54,725 - INFO - Finished processing chromosome chr3
2022-05-04 09:52:00,930 - INFO - Finished processing chromosome chrM
2022-05-04 09:52:04,071 - INFO - Finished processing chromosome chr6
2022-05-04 09:52:08,825 - INFO - Finished processing chromosome chr4
2022-05-04 09:52:20,599 - INFO - Finished processing chromosome chrY
2022-05-04 09:52:28,018 - INFO - Finished processing chromosome chr9
2022-05-04 09:52:31,006 - INFO - Finished processing chromosome chr5
2022-05-04 09:52:54,097 - INFO - Finished processing chromosome chr1
2022-05-04 09:53:01,313 - INFO - Finished processing chromosome chr18
2022-05-04 09:53:01,466 - INFO - Finished processing chromosome chr11
2022-05-04 09:53:08,309 - INFO - Finished processing chromosome chr16
2022-05-04 09:53:09,271 - INFO - Finished processing chromosome chr19
2022-05-04 09:53:13,969 - INFO - Finished processing chromosome chr2
2022-05-04 09:53:29,508 - INFO - Finished processing chromosome chr15
2022-05-04 09:53:32,189 - INFO - Finished processing chromosome chr7
2022-05-04 09:53:34,194 - INFO - Resolving multimappers
2022-05-04 09:53:38,750 - INFO - Finishing read assignment, total assignments 730368, polyA percentage 81.4
2022-05-04 09:53:39,108 - INFO - Read assignments files saved to PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save*. 
2022-05-04 09:53:39,108 - INFO - To keep these intermediate files for debug purposes use --keep_tmp flag
2022-05-04 09:53:39,260 - INFO - Total alignments processed: 730368, polyA tail detected in 594570 (81.4%)
2022-05-04 09:53:40,161 - INFO - Processing assigned reads 00_PMK1_sorted
2022-05-04 09:53:40,733 - INFO - Processing chromosome chr7
2022-05-04 09:53:40,738 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr7
2022-05-04 09:53:41,199 - INFO - Processing chromosome chr2
2022-05-04 09:53:41,204 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr2
2022-05-04 09:53:41,630 - INFO - Processing chromosome chr1
2022-05-04 09:53:41,635 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr1
2022-05-04 09:53:41,884 - INFO - Processing chromosome chr5
2022-05-04 09:53:41,888 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr5
2022-05-04 09:53:42,536 - INFO - Processing chromosome chr9
2022-05-04 09:53:42,541 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr9
2022-05-04 09:53:43,368 - INFO - Processing chromosome chr6
2022-05-04 09:53:43,373 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr6
2022-05-04 09:53:43,751 - INFO - Processing chromosome chr12
2022-05-04 09:53:43,755 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr12
2022-05-04 09:53:44,428 - INFO - Processing chromosome chr3
2022-05-04 09:53:44,434 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr3
2022-05-04 09:53:45,442 - INFO - Processing chromosome chr11
2022-05-04 09:53:45,450 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr11
2022-05-04 09:53:47,026 - INFO - Processing chromosome chr4
2022-05-04 09:53:47,033 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr4
2022-05-04 09:53:47,457 - INFO - Processing chromosome chr17
2022-05-04 09:53:47,463 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr17
2022-05-04 09:53:48,610 - INFO - Processing chromosome chr8
2022-05-04 09:53:48,614 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr8
2022-05-04 09:53:49,549 - INFO - Processing chromosome chr14
2022-05-04 09:53:49,554 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr14
2022-05-04 09:53:50,985 - INFO - Processing chromosome chr10
2022-05-04 09:53:50,991 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr10
2022-05-04 09:53:52,301 - INFO - Processing chromosome chr13
2022-05-04 09:53:52,306 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr13
2022-05-04 09:53:53,228 - INFO - Processing chromosome chrX
2022-05-04 09:53:53,232 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chrX
2022-05-04 09:53:59,394 - INFO - Finished processing chromosome chr12
2022-05-04 09:54:00,311 - INFO - Processing chromosome chr15
2022-05-04 09:54:00,315 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr15
2022-05-04 09:54:04,057 - INFO - Finished processing chromosome chrX
2022-05-04 09:54:05,126 - INFO - Processing chromosome chr16
2022-05-04 09:54:05,130 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr16
2022-05-04 09:54:14,416 - INFO - Finished processing chromosome chr5
2022-05-04 09:54:14,760 - INFO - Finished processing chromosome chr9
2022-05-04 09:54:14,776 - INFO - Finished processing chromosome chr6
2022-05-04 09:54:15,527 - INFO - Processing chromosome chr19
2022-05-04 09:54:15,532 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr19
2022-05-04 09:54:16,261 - INFO - Finished processing chromosome chr14
2022-05-04 09:54:16,355 - INFO - Finished processing chromosome chr13
2022-05-04 09:54:16,561 - INFO - Processing chromosome chr18
2022-05-04 09:54:16,565 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chr18
2022-05-04 09:54:17,102 - INFO - Processing chromosome chrY
2022-05-04 09:54:17,106 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chrY
2022-05-04 09:54:17,779 - INFO - Processing chromosome chrM
2022-05-04 09:54:17,783 - INFO - Loading read assignments from PMK1/00_PMK1_sorted/aux/00_PMK1_sorted.save_chrM
2022-05-04 09:54:18,001 - INFO - Finished processing chromosome chrY
2022-05-04 09:54:18,540 - INFO - Finished processing chromosome chr8
2022-05-04 09:54:18,834 - INFO - Finished processing chromosome chr2
2022-05-04 09:54:19,187 - INFO - Finished processing chromosome chr4
2022-05-04 09:54:19,597 - INFO - Finished processing chromosome chr17
2022-05-04 09:54:20,687 - INFO - Finished processing chromosome chr16
2022-05-04 09:54:21,046 - INFO - Finished processing chromosome chr1
2022-05-04 09:54:21,127 - INFO - Finished processing chromosome chr7
2022-05-04 09:54:22,234 - INFO - Finished processing chromosome chr10
2022-05-04 09:54:22,348 - INFO - Finished processing chromosome chr3
2022-05-04 09:54:23,127 - INFO - Finished processing chromosome chrM
2022-05-04 09:54:24,705 - INFO - Finished processing chromosome chr15
2022-05-04 09:54:25,102 - INFO - Finished processing chromosome chr18
2022-05-04 09:54:26,396 - INFO - Finished processing chromosome chr19
2022-05-04 09:54:27,549 - INFO - Finished processing chromosome chr11
2022-05-04 09:54:29,388 - INFO - Scale factor for group NA = 2.19
2022-05-04 09:54:29,583 - INFO - Scale factor for group NA = 2.39
2022-05-04 09:54:30,161 - INFO - Scale factor for group NA = 2.26
2022-05-04 09:54:30,196 - INFO - Gene counts are stored in PMK1/00_PMK1_sorted/00_PMK1_sorted.gene_counts.tsv
2022-05-04 09:54:30,197 - INFO - Transcript counts are stored in PMK1/00_PMK1_sorted/00_PMK1_sorted.transcript_counts.tsv
2022-05-04 09:54:30,197 - INFO - Read assignments are stored in PMK1/00_PMK1_sorted/00_PMK1_sorted.read_assignments.tsv
2022-05-04 09:54:30,197 - INFO - Read assignment statistics
2022-05-04 09:54:30,197 - INFO - ambiguous: 95121
2022-05-04 09:54:30,197 - INFO - inconsistent: 235810
2022-05-04 09:54:30,197 - INFO - noninformative: 26222
2022-05-04 09:54:30,197 - INFO - unique: 313135
2022-05-04 09:54:30,197 - INFO - unique_minor_difference: 60080
2022-05-04 09:54:30,197 - INFO - Transcript model file PMK1/00_PMK1_sorted/00_PMK1_sorted.transcript_models.gtf
2022-05-04 09:54:30,197 - INFO - Transcript model statistics
2022-05-04 09:54:30,197 - INFO - known: 10378
2022-05-04 09:54:30,197 - INFO - novel_in_catalog: 170
2022-05-04 09:54:30,198 - INFO - novel_not_in_catalog: 79
2022-05-04 09:54:30,959 - INFO - Processed sample 00_PMK1_sorted
2022-05-04 09:54:30,961 - INFO - Processed 1 sample
2022-05-04 09:54:30,961 - INFO -  === IsoQuant pipeline finished ===