2024-04-22 15:42:40,212 NanoComp 1.19.3 started with arguments Namespace(bam=None, barcoded=False, colors=None, cram=None, dpi=100, fasta=None, fastq=['bc_1_all_filt.sorted.bam', 'bc_2_all_filt.sorted.bam', 'bc_3_all_filt.sorted.bam', 'bc_4_all_filt.sorted.bam', 'bc_5_all_filt.sorted.bam', 'bc_6_all_filt.sorted.bam', 'bc_10_all_filt.sorted.bam', 'bc_11_all_filt.sorted.bam', 'bc_12_all_filt.sorted.bam', 'bc_13_all_filt.sorted.bam', 'bc_14_all_filt.sorted.bam', 'bc_15_all_filt.sorted.bam'], fastq_rich=None, feather=None, format=['pdf'], maxlength=None, minlength=None, names=['Day2_1', 'Day2_2', 'Day2_3', 'Day5_1', 'Day5_2', 'Day5_3', 'Day9_1', 'Day9_2', 'Day9_3', 'Day15_1', 'Day15_2', 'Day15_3'], no_static=False, outdir='compare-runs', path='compare-runs/', pickle=None, plot='box', prefix='', raw=False, readtype='1D', split_runs=False, store=False, summary=None, threads=4, title=None, tsv_stats=False, ubam=None, verbose=False)
2024-04-22 15:42:40,213 Python version is: 3.7.2 (default, Jul 30 2019, 16:21:53)  [GCC 8.2.0]
2024-04-22 15:42:40,277 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,278 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,279 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,280 INPUT ERROR: Unrecognized file extension bc_1_all_filt.sorted.bam
2024-04-22 15:42:40,280 INPUT ERROR: Unrecognized file extension bc_2_all_filt.sorted.bam
2024-04-22 15:42:40,281 INPUT ERROR: Unrecognized file extension bc_3_all_filt.sorted.bam
2024-04-22 15:42:40,284 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,285 INPUT ERROR: Unrecognized file extension bc_4_all_filt.sorted.bam
2024-04-22 15:42:40,289 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,290 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,290 INPUT ERROR: Unrecognized file extension bc_5_all_filt.sorted.bam
2024-04-22 15:42:40,291 INPUT ERROR: Unrecognized file extension bc_6_all_filt.sorted.bam
2024-04-22 15:42:40,292 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,292 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,292 INPUT ERROR: Unrecognized file extension bc_10_all_filt.sorted.bam
2024-04-22 15:42:40,293 INPUT ERROR: Unrecognized file extension bc_11_all_filt.sorted.bam
2024-04-22 15:42:40,294 Nanoget: Starting to collect statistics from plain fastq file.
2024-04-22 15:42:40,295 INPUT ERROR: Unrecognized file extension bc_12_all_filt.sorted.bam
2024-04-22 15:42:53,253 NanoComp 1.19.3 started with arguments Namespace(bam=['bc_1_all_filt.sorted.bam', 'bc_2_all_filt.sorted.bam', 'bc_3_all_filt.sorted.bam', 'bc_4_all_filt.sorted.bam', 'bc_5_all_filt.sorted.bam', 'bc_6_all_filt.sorted.bam', 'bc_10_all_filt.sorted.bam', 'bc_11_all_filt.sorted.bam', 'bc_12_all_filt.sorted.bam', 'bc_13_all_filt.sorted.bam', 'bc_14_all_filt.sorted.bam', 'bc_15_all_filt.sorted.bam'], barcoded=False, colors=None, cram=None, dpi=100, fasta=None, fastq=None, fastq_rich=None, feather=None, format=['pdf'], maxlength=None, minlength=None, names=['Day2_1', 'Day2_2', 'Day2_3', 'Day5_1', 'Day5_2', 'Day5_3', 'Day9_1', 'Day9_2', 'Day9_3', 'Day15_1', 'Day15_2', 'Day15_3'], no_static=False, outdir='compare-runs', path='compare-runs/', pickle=None, plot='box', prefix='', raw=False, readtype='1D', split_runs=False, store=False, summary=None, threads=4, title=None, tsv_stats=False, ubam=None, verbose=False)
2024-04-22 15:42:53,253 Python version is: 3.7.2 (default, Jul 30 2019, 16:21:53)  [GCC 8.2.0]
2024-04-22 15:42:53,301 Nanoget: Starting to collect statistics from bam file bc_1_all_filt.sorted.bam.
2024-04-22 15:42:53,302 Nanoget: Starting to collect statistics from bam file bc_2_all_filt.sorted.bam.
2024-04-22 15:42:53,304 Nanoget: Starting to collect statistics from bam file bc_3_all_filt.sorted.bam.
2024-04-22 15:42:53,305 Nanoget: Starting to collect statistics from bam file bc_4_all_filt.sorted.bam.
2024-04-22 15:42:53,348 Nanoget: Bam file bc_4_all_filt.sorted.bam contains 458735 mapped and 0 unmapped reads.
2024-04-22 15:42:53,353 Nanoget: Bam file bc_3_all_filt.sorted.bam contains 390024 mapped and 0 unmapped reads.
2024-04-22 15:42:53,356 Nanoget: Bam file bc_2_all_filt.sorted.bam contains 255749 mapped and 0 unmapped reads.
2024-04-22 15:42:53,370 Nanoget: Bam file bc_1_all_filt.sorted.bam contains 367760 mapped and 0 unmapped reads.
2024-04-22 15:46:04,512 Nanoget: bam bc_2_all_filt.sorted.bam contains 255749 primary alignments.
2024-04-22 15:46:14,741 Reduced DataFrame memory usage from 36.34128665924072Mb to 28.78034782409668Mb
2024-04-22 15:46:15,395 Nanoget: Starting to collect statistics from bam file bc_5_all_filt.sorted.bam.
2024-04-22 15:46:15,462 Nanoget: Bam file bc_5_all_filt.sorted.bam contains 352303 mapped and 0 unmapped reads.
2024-04-22 15:46:21,960 Nanoget: bam bc_1_all_filt.sorted.bam contains 367760 primary alignments.
2024-04-22 15:46:36,419 Reduced DataFrame memory usage from 52.25776672363281Mb to 41.385345458984375Mb
2024-04-22 15:46:37,460 Nanoget: Starting to collect statistics from bam file bc_6_all_filt.sorted.bam.
2024-04-22 15:46:37,506 Nanoget: Bam file bc_6_all_filt.sorted.bam contains 142405 mapped and 0 unmapped reads.
2024-04-22 15:47:42,973 Nanoget: bam bc_6_all_filt.sorted.bam contains 142405 primary alignments.
2024-04-22 15:47:48,422 Reduced DataFrame memory usage from 20.235390663146973Mb to 16.02534294128418Mb
2024-04-22 15:47:48,777 Nanoget: Starting to collect statistics from bam file bc_10_all_filt.sorted.bam.
2024-04-22 15:47:49,000 Nanoget: Bam file bc_10_all_filt.sorted.bam contains 581331 mapped and 0 unmapped reads.
2024-04-22 15:48:16,807 Nanoget: bam bc_3_all_filt.sorted.bam contains 390024 primary alignments.
2024-04-22 15:48:32,336 Reduced DataFrame memory usage from 55.421424865722656Mb to 43.89079284667969Mb
2024-04-22 15:48:33,287 Nanoget: Starting to collect statistics from bam file bc_11_all_filt.sorted.bam.
2024-04-22 15:48:33,351 Nanoget: Bam file bc_11_all_filt.sorted.bam contains 430745 mapped and 0 unmapped reads.
2024-04-22 15:49:55,113 Nanoget: bam bc_4_all_filt.sorted.bam contains 458735 primary alignments.
2024-04-22 15:50:13,647 Reduced DataFrame memory usage from 65.18508434295654Mb to 51.62308692932129Mb
2024-04-22 15:50:14,987 Nanoget: Starting to collect statistics from bam file bc_12_all_filt.sorted.bam.
2024-04-22 15:50:15,061 Nanoget: Bam file bc_12_all_filt.sorted.bam contains 692071 mapped and 0 unmapped reads.
2024-04-22 15:50:34,960 Nanoget: bam bc_5_all_filt.sorted.bam contains 352303 primary alignments.
2024-04-22 15:50:48,561 Reduced DataFrame memory usage from 50.06136608123779Mb to 40.31787872314453Mb
2024-04-22 15:50:49,642 Nanoget: Starting to collect statistics from bam file bc_13_all_filt.sorted.bam.
2024-04-22 15:50:49,710 Nanoget: Bam file bc_13_all_filt.sorted.bam contains 159750 mapped and 0 unmapped reads.
2024-04-22 15:52:29,200 Nanoget: bam bc_13_all_filt.sorted.bam contains 159750 primary alignments.
2024-04-22 15:52:35,277 Reduced DataFrame memory usage from 22.700071334838867Mb to 17.977237701416016Mb
2024-04-22 15:52:35,702 Nanoget: Starting to collect statistics from bam file bc_14_all_filt.sorted.bam.
2024-04-22 15:52:35,760 Nanoget: Bam file bc_14_all_filt.sorted.bam contains 101437 mapped and 0 unmapped reads.
2024-04-22 15:52:47,888 Nanoget: bam bc_11_all_filt.sorted.bam contains 430745 primary alignments.
2024-04-22 15:53:04,568 Reduced DataFrame memory usage from 61.20777606964111Mb to 48.4732723236084Mb
2024-04-22 15:53:05,702 Nanoget: Starting to collect statistics from bam file bc_15_all_filt.sorted.bam.
2024-04-22 15:53:05,779 Nanoget: Bam file bc_15_all_filt.sorted.bam contains 261864 mapped and 0 unmapped reads.
2024-04-22 15:53:44,572 Nanoget: bam bc_14_all_filt.sorted.bam contains 101437 primary alignments.
2024-04-22 15:53:48,438 Reduced DataFrame memory usage from 14.413941383361816Mb to 11.415067672729492Mb
2024-04-22 15:55:06,587 Nanoget: bam bc_15_all_filt.sorted.bam contains 261864 primary alignments.
2024-04-22 15:55:14,068 Reduced DataFrame memory usage from 37.21021270751953Mb to 29.96795654296875Mb
2024-04-22 15:55:14,433 Nanoget: bam bc_10_all_filt.sorted.bam contains 581331 primary alignments.
2024-04-22 15:55:25,434 Reduced DataFrame memory usage from 82.6056661605835Mb to 65.41925239562988Mb
2024-04-22 15:56:17,086 Nanoget: bam bc_12_all_filt.sorted.bam contains 692071 primary alignments.
2024-04-22 15:56:23,702 Reduced DataFrame memory usage from 98.34154033660889Mb to 77.8812198638916Mb
2024-04-22 15:56:25,859 Nanoget: Gathered all metrics of 4194174 reads
2024-04-22 15:56:25,861 Using sequenced read lengths for plotting.
2024-04-22 15:56:38,359 NanoComp: Creating barplots for number of reads and total throughput.
2024-04-22 15:56:44,156 Saved compare-runs/NanoComp_number_of_reads  as pdf (or png for --legacy)
2024-04-22 15:56:45,912 Saved compare-runs/NanoComp_total_throughput  as pdf (or png for --legacy)
2024-04-22 15:56:47,379 Saved compare-runs/NanoComp_N50  as pdf (or png for --legacy)
2024-04-22 15:56:47,576 NanoComp: Creating box plot for lengths.
2024-04-22 15:56:52,379 Saved compare-runs/NanoComp_lengths_box  as pdf (or png for --legacy)
2024-04-22 15:56:52,509 NanoComp: Creating box plot for log length.
2024-04-22 15:56:56,533 Saved compare-runs/NanoComp_log_length_box  as pdf (or png for --legacy)
2024-04-22 15:56:56,611 NanoComp: Creating box plot for quals.
2024-04-22 15:57:00,437 Saved compare-runs/NanoComp_quals_box  as pdf (or png for --legacy)
2024-04-22 15:57:00,581 NanoComp: Creating box plot for percentIdentity.
2024-04-22 15:57:06,152 Saved compare-runs/NanoComp_percentIdentity_box  as pdf (or png for --legacy)
2024-04-22 15:57:08,315 Saved compare-runs/NanoComp_OverlayHistogram_Identity  as pdf (or png for --legacy)
2024-04-22 15:57:10,184 Saved compare-runs/NanoComp_OverlayHistogram_PhredScore  as pdf (or png for --legacy)
2024-04-22 15:57:11,907 Saved compare-runs/NanoComp_OverlayHistogram  as pdf (or png for --legacy)
2024-04-22 15:57:13,893 Saved compare-runs/NanoComp_OverlayHistogram_Normalized  as pdf (or png for --legacy)
2024-04-22 15:57:15,735 Saved compare-runs/NanoComp_OverlayLogHistogram  as pdf (or png for --legacy)
2024-04-22 15:57:17,803 Saved compare-runs/NanoComp_OverlayLogHistogram_Normalized  as pdf (or png for --legacy)
2024-04-22 15:57:17,881 Writing html report.
2024-04-22 15:57:18,005 Succesfully processed all input.