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/SK2_sorted.bam --data_type nanopore -o SK2
2022-05-04 08:32:47,648 - WARNING - SK2/00_SK2_sorted folder already exists, some files may be overwritten
2022-05-04 08:32:47,650 - WARNING - SK2/00_SK2_sorted/aux folder already exists, some files may be overwritten
2022-05-04 08:32:47,657 - INFO -  === IsoQuant pipeline started === 
2022-05-04 08:32:47,662 - INFO - Gene annotation file found. Using /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/SK1/gencode.v39.annotation.db
2022-05-04 08:32:47,663 - INFO - Loading gene database from /nfs/users/enovoa/imilenkovic/isoquant/AnnaGiulia/SK1/gencode.v39.annotation.db
2022-05-04 08:32:47,687 - INFO - Loading reference genome from /users/enovoa/imilenkovic/references/GRCh38.primary_assembly.genome.fa
2022-05-04 08:33:26,622 - INFO - Processing 1 sample
2022-05-04 08:33:26,623 - INFO - Processing sample 00_SK2_sorted
2022-05-04 08:33:26,623 - INFO - Sample has 1 BAM file: /no_backup_isis/enovoa/nextflow_outputs/Anna_Giulia/cDNA100122_human_genome_no_discovery/bambu/SK2_sorted.bam
2022-05-04 08:33:26,623 - INFO - Assigning reads to isoforms
2022-05-04 08:33:27,687 - INFO - Processing chromosome chr19
2022-05-04 08:33:27,733 - INFO - Processing chromosome chr1
2022-05-04 08:33:27,853 - INFO - Processing chromosome chr17
2022-05-04 08:33:28,357 - INFO - Processing chromosome chr2
2022-05-04 08:33:28,487 - INFO - Processing chromosome chr11
2022-05-04 08:33:28,687 - INFO - Processing chromosome chr12
2022-05-04 08:33:28,830 - INFO - Processing chromosome chr16
2022-05-04 08:33:29,231 - INFO - Processing chromosome chr3
2022-05-04 08:33:29,595 - INFO - Processing chromosome chr7
2022-05-04 08:33:29,759 - INFO - Processing chromosome chr14
2022-05-04 08:33:30,435 - INFO - Processing chromosome chr6
2022-05-04 08:33:30,493 - INFO - Processing chromosome chr15
2022-05-04 08:33:30,975 - INFO - Processing chromosome chr5
2022-05-04 08:33:31,168 - INFO - Processing chromosome chr10
2022-05-04 08:33:31,797 - INFO - Processing chromosome chr8
2022-05-04 08:33:32,409 - INFO - Processing chromosome chr4
2022-05-04 08:38:19,317 - INFO - Finished processing chromosome chr4
2022-05-04 08:38:20,490 - INFO - Processing chromosome chr9
2022-05-04 08:38:30,851 - INFO - Finished processing chromosome chr14
2022-05-04 08:38:31,833 - INFO - Processing chromosome chrX
2022-05-04 08:38:56,057 - INFO - Finished processing chromosome chr8
2022-05-04 08:38:56,664 - INFO - Processing chromosome chr22
2022-05-04 08:39:02,896 - INFO - Finished processing chromosome chr10
2022-05-04 08:39:03,382 - INFO - Processing chromosome chr20
2022-05-04 08:39:18,808 - INFO - Finished processing chromosome chr16
2022-05-04 08:39:19,975 - INFO - Processing chromosome chr13
2022-05-04 08:39:53,232 - INFO - Finished processing chromosome chr7
2022-05-04 08:39:54,267 - INFO - Processing chromosome chr18
2022-05-04 08:40:01,477 - INFO - Finished processing chromosome chr15
2022-05-04 08:40:02,067 - INFO - Processing chromosome chr21
2022-05-04 08:40:42,766 - INFO - Finished processing chromosome chr6
2022-05-04 08:40:43,188 - INFO - Processing chromosome chrY
2022-05-04 08:40:51,631 - INFO - Finished processing chromosome chr17
2022-05-04 08:40:52,189 - INFO - Processing chromosome chrM
2022-05-04 08:41:10,746 - INFO - Finished processing chromosome chr5
2022-05-04 08:41:12,749 - INFO - Finished processing chromosome chrY
2022-05-04 08:41:23,800 - INFO - Finished processing chromosome chr19
2022-05-04 08:41:33,506 - INFO - Finished processing chromosome chrM
2022-05-04 08:41:39,032 - INFO - Finished processing chromosome chr21
2022-05-04 08:41:50,886 - INFO - Finished processing chromosome chr3
2022-05-04 08:41:55,278 - INFO - Finished processing chromosome chr13
2022-05-04 08:41:55,553 - INFO - Finished processing chromosome chr22
2022-05-04 08:41:58,285 - INFO - Finished processing chromosome chr12
2022-05-04 08:41:58,867 - INFO - Finished processing chromosome chr18
2022-05-04 08:42:21,513 - INFO - Finished processing chromosome chr11
2022-05-04 08:42:22,104 - INFO - Finished processing chromosome chrX
2022-05-04 08:42:23,454 - INFO - Finished processing chromosome chr20
2022-05-04 08:42:29,955 - INFO - Finished processing chromosome chr9
2022-05-04 08:43:05,878 - INFO - Finished processing chromosome chr2
2022-05-04 08:43:53,997 - INFO - Finished processing chromosome chr1
2022-05-04 08:43:55,811 - INFO - Resolving multimappers
2022-05-04 08:44:01,453 - INFO - Finishing read assignment, total assignments 709990, polyA percentage 81.4
2022-05-04 08:44:02,374 - INFO - Read assignments files saved to SK2/00_SK2_sorted/aux/00_SK2_sorted.save*. 
2022-05-04 08:44:02,374 - INFO - To keep these intermediate files for debug purposes use --keep_tmp flag
2022-05-04 08:44:02,663 - INFO - Total alignments processed: 709990, polyA tail detected in 577579 (81.4%)
2022-05-04 08:44:03,001 - INFO - Processing assigned reads 00_SK2_sorted
2022-05-04 08:44:04,029 - INFO - Processing chromosome chr19
2022-05-04 08:44:04,035 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr19
2022-05-04 08:44:04,067 - INFO - Processing chromosome chr1
2022-05-04 08:44:04,072 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr1
2022-05-04 08:44:04,144 - INFO - Processing chromosome chr17
2022-05-04 08:44:04,149 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr17
2022-05-04 08:44:04,800 - INFO - Processing chromosome chr2
2022-05-04 08:44:04,808 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr2
2022-05-04 08:44:05,194 - INFO - Processing chromosome chr11
2022-05-04 08:44:05,199 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr11
2022-05-04 08:44:05,887 - INFO - Processing chromosome chr12
2022-05-04 08:44:05,892 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr12
2022-05-04 08:44:06,239 - INFO - Processing chromosome chr16
2022-05-04 08:44:06,244 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr16
2022-05-04 08:44:07,194 - INFO - Processing chromosome chr3
2022-05-04 08:44:07,198 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr3
2022-05-04 08:44:07,444 - INFO - Processing chromosome chr7
2022-05-04 08:44:07,449 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr7
2022-05-04 08:44:07,539 - INFO - Processing chromosome chr14
2022-05-04 08:44:07,544 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr14
2022-05-04 08:44:09,163 - INFO - Processing chromosome chr15
2022-05-04 08:44:09,167 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr15
2022-05-04 08:44:09,262 - INFO - Processing chromosome chr6
2022-05-04 08:44:09,266 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr6
2022-05-04 08:44:11,202 - INFO - Processing chromosome chr5
2022-05-04 08:44:11,211 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr5
2022-05-04 08:44:11,531 - INFO - Processing chromosome chr10
2022-05-04 08:44:11,543 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr10
2022-05-04 08:44:12,843 - INFO - Processing chromosome chr8
2022-05-04 08:44:12,848 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr8
2022-05-04 08:44:13,257 - INFO - Processing chromosome chr4
2022-05-04 08:44:13,263 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr4
2022-05-04 08:44:25,902 - INFO - Finished processing chromosome chr14
2022-05-04 08:44:26,844 - INFO - Processing chromosome chr9
2022-05-04 08:44:26,849 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr9
2022-05-04 08:44:27,022 - INFO - Finished processing chromosome chr4
2022-05-04 08:44:27,830 - INFO - Processing chromosome chrX
2022-05-04 08:44:27,835 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chrX
2022-05-04 08:44:28,172 - INFO - Finished processing chromosome chr7
2022-05-04 08:44:28,547 - INFO - Processing chromosome chr22
2022-05-04 08:44:28,550 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr22
2022-05-04 08:44:29,775 - INFO - Finished processing chromosome chr16
2022-05-04 08:44:30,261 - INFO - Processing chromosome chr20
2022-05-04 08:44:30,266 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr20
2022-05-04 08:44:36,762 - INFO - Finished processing chromosome chr17
2022-05-04 08:44:37,609 - INFO - Processing chromosome chr13
2022-05-04 08:44:37,613 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr13
2022-05-04 08:44:40,878 - INFO - Finished processing chromosome chr2
2022-05-04 08:44:41,142 - INFO - Finished processing chromosome chr22
2022-05-04 08:44:41,516 - INFO - Processing chromosome chr18
2022-05-04 08:44:41,520 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr18
2022-05-04 08:44:41,539 - INFO - Processing chromosome chr21
2022-05-04 08:44:41,543 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chr21
2022-05-04 08:44:46,534 - INFO - Finished processing chromosome chr11
2022-05-04 08:44:46,850 - INFO - Finished processing chromosome chr21
2022-05-04 08:44:47,079 - INFO - Finished processing chromosome chrX
2022-05-04 08:44:47,109 - INFO - Processing chromosome chrY
2022-05-04 08:44:47,114 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chrY
2022-05-04 08:44:47,682 - INFO - Finished processing chromosome chrY
2022-05-04 08:44:48,236 - INFO - Processing chromosome chrM
2022-05-04 08:44:48,239 - INFO - Loading read assignments from SK2/00_SK2_sorted/aux/00_SK2_sorted.save_chrM
2022-05-04 08:44:48,740 - INFO - Finished processing chromosome chr13
2022-05-04 08:44:49,541 - INFO - Finished processing chromosome chr18
2022-05-04 08:44:50,402 - INFO - Finished processing chromosome chr8
2022-05-04 08:44:51,362 - INFO - Finished processing chromosome chr20
2022-05-04 08:44:51,544 - INFO - Finished processing chromosome chr1
2022-05-04 08:44:51,742 - INFO - Finished processing chromosome chr3
2022-05-04 08:44:51,961 - INFO - Finished processing chromosome chr9
2022-05-04 08:44:52,374 - INFO - Finished processing chromosome chr5
2022-05-04 08:44:52,962 - INFO - Finished processing chromosome chr10
2022-05-04 08:44:53,638 - INFO - Finished processing chromosome chr15
2022-05-04 08:44:54,431 - INFO - Finished processing chromosome chrM
2022-05-04 08:44:54,711 - INFO - Finished processing chromosome chr6
2022-05-04 08:44:57,645 - INFO - Finished processing chromosome chr12
2022-05-04 08:45:00,155 - INFO - Finished processing chromosome chr19
2022-05-04 08:45:05,127 - INFO - Scale factor for group NA = 2.19
2022-05-04 08:45:05,488 - INFO - Scale factor for group NA = 2.44
2022-05-04 08:45:06,878 - INFO - Scale factor for group NA = 2.19
2022-05-04 08:45:06,951 - INFO - Gene counts are stored in SK2/00_SK2_sorted/00_SK2_sorted.gene_counts.tsv
2022-05-04 08:45:06,951 - INFO - Transcript counts are stored in SK2/00_SK2_sorted/00_SK2_sorted.transcript_counts.tsv
2022-05-04 08:45:06,951 - INFO - Read assignments are stored in SK2/00_SK2_sorted/00_SK2_sorted.read_assignments.tsv
2022-05-04 08:45:06,951 - INFO - Read assignment statistics
2022-05-04 08:45:06,952 - INFO - ambiguous: 127304
2022-05-04 08:45:06,952 - INFO - inconsistent: 228986
2022-05-04 08:45:06,952 - INFO - noninformative: 12923
2022-05-04 08:45:06,952 - INFO - unique: 282068
2022-05-04 08:45:06,952 - INFO - unique_minor_difference: 58709
2022-05-04 08:45:06,952 - INFO - Transcript model file SK2/00_SK2_sorted/00_SK2_sorted.transcript_models.gtf
2022-05-04 08:45:06,952 - INFO - Transcript model statistics
2022-05-04 08:45:06,952 - INFO - known: 13366
2022-05-04 08:45:06,953 - INFO - novel_in_catalog: 263
2022-05-04 08:45:06,953 - INFO - novel_not_in_catalog: 98
2022-05-04 08:45:07,813 - INFO - Processed sample 00_SK2_sorted
2022-05-04 08:45:07,814 - INFO - Processed 1 sample
2022-05-04 08:45:07,814 - INFO -  === IsoQuant pipeline finished ===