merged maain with exp

.test/stats_out/joblog/joblog_stat.txt

@@ -0,0 +1,58 @@
+project_dir: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out
+input_fastq: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/test_data
+JobNr: 1
+Threads: 1
+project_dir: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out
+input_fastq: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/test_data
+JobNr: 1
+Threads: 1
+Moving sample1
+Moving sample1
+cp: cannot create regular file '/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample1/sample1.fastq.gz': File exists
+Moving sample3
+Moving sample3
+Moving sample2
+Moving sample2
+cp: cannot create regular file '/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample2/sample2.fastq.gz': File exists
+Finished moving and unzipping
+Finished moving and unzipping
+Processing files in: sample1
+Processing files in: sample1
+Merged all files in sample1
+Merged all files in sample1
+Processing files in: sample2
+Processing files in: sample2
+Merged all files in sample2
+Processing files in: sample3
+cat: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample2/sample2_merged.fastq: input file is output file
+Merged all files in sample3
+Merged all files in sample2
+Processing files in: sample3
+created directory for sample1 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+created directory for sample2 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+cat: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample3/sample3_merged.fastq: input file is output file
+Merged all files in sample3
+created directory for sample3 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+created directory for sample1 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+created directory for sample2 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+created directory for sample3 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats
+Creating plots and stats for sample1 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample1/sample1_merged.fastq
+Finished plots and stats for sample1
+Creating plots and stats for sample1 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample1/sample1_merged.fastq
+Finished plots and stats for sample1
+Creating plots and stats for sample2 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample2
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample2/sample2_merged.fastq
+Finished plots and stats for sample2
+Creating plots and stats for sample2 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample2
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample2/sample2_merged.fastq
+Finished plots and stats for sample2
+Creating plots and stats for sample3 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample3
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample3/sample3_merged.fastq
+Finished plots and stats for sample3
+Creating plots and stats for sample3 in /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample3
+Processing file: /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample3/sample3_merged.fastq
+Finished plots and stats for sample3
+Check your amplicon size and quality before setting parameters for chopper filtering, used in the snakemake workflow. Filtering settings can be changed in the config file. "config/config.yaml"
+Check your amplicon size and quality before setting parameters for chopper filtering, used in the snakemake workflow. Filtering settings can be changed in the config file. "config/config.yaml"

.test/stats_out/stats/sample1/NanoPlot_20240602_1806.log

@@ -0,0 +1,44 @@
+2024-06-02 18:06:25,445 NanoPlot 1.42.0 started with arguments Namespace(threads=1, verbose=False, store=False, raw=False, huge=False, outdir='/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1', no_static=False, prefix='', tsv_stats=False, only_report=False, info_in_report=False, maxlength=None, minlength=None, drop_outliers=False, downsample=None, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='#4CB391', colormap='Greens', format=['png'], plots=['dot'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=['/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample1/sample1_merged.fastq'], fasta=None, fastq_rich=None, fastq_minimal=None, summary=None, bam=None, ubam=None, cram=None, pickle=None, feather=None, path='/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/')
+2024-06-02 18:06:25,445 NanoPlot 1.42.0 started with arguments Namespace(threads=1, verbose=False, store=False, raw=False, huge=False, outdir='/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1', no_static=False, prefix='', tsv_stats=False, only_report=False, info_in_report=False, maxlength=None, minlength=None, drop_outliers=False, downsample=None, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='#4CB391', colormap='Greens', format=['png'], plots=['dot'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=False, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=['/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/fastqs/sample1/sample1_merged.fastq'], fasta=None, fastq_rich=None, fastq_minimal=None, summary=None, bam=None, ubam=None, cram=None, pickle=None, feather=None, path='/home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/')
+2024-06-02 18:06:25,445 Python version is: 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0]
+2024-06-02 18:06:25,446 Python version is: 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0]
+2024-06-02 18:06:25,843 Nanoget: Starting to collect statistics from plain fastq file.
+2024-06-02 18:06:25,846 Nanoget: Starting to collect statistics from plain fastq file.
+2024-06-02 18:06:26,827 Reduced DataFrame memory usage from 0.015380859375Mb to 0.015380859375Mb
+2024-06-02 18:06:26,830 Reduced DataFrame memory usage from 0.015380859375Mb to 0.015380859375Mb
+2024-06-02 18:06:26,843 Nanoget: Gathered all metrics of 1000 reads
+2024-06-02 18:06:26,846 Nanoget: Gathered all metrics of 1000 reads
+2024-06-02 18:06:26,856 Calculated statistics
+2024-06-02 18:06:26,857 Using sequenced read lengths for plotting.
+2024-06-02 18:06:26,859 Calculated statistics
+2024-06-02 18:06:26,860 Using sequenced read lengths for plotting.
+2024-06-02 18:06:26,884 NanoPlot:  Valid color #4CB391.
+2024-06-02 18:06:26,884 NanoPlot:  Valid color #4CB391.
+2024-06-02 18:06:26,884 NanoPlot:  Valid colormap Greens.
+2024-06-02 18:06:26,884 NanoPlot:  Valid colormap Greens.
+2024-06-02 18:06:26,886 NanoPlot:  Creating length plots for Read length.
+2024-06-02 18:06:26,886 NanoPlot:  Creating length plots for Read length.
+2024-06-02 18:06:26,886 NanoPlot:  Using 1000 reads maximum of 1564bp.
+2024-06-02 18:06:26,886 NanoPlot:  Using 1000 reads maximum of 1564bp.
+2024-06-02 18:06:39,655 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/WeightedHistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:39,658 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/WeightedHistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:41,160 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/WeightedLogTransformed_HistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:41,270 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/WeightedLogTransformed_HistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:42,232 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Non_weightedHistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:42,377 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Non_weightedHistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:43,219 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Non_weightedLogTransformed_HistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:06:43,381 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Non_weightedLogTransformed_HistogramReadlength  as png (or png for --legacy)
+2024-06-02 18:07:01,740 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Yield_By_Length  as png (or png for --legacy)
+2024-06-02 18:07:01,740 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/Yield_By_Length  as png (or png for --legacy)
+2024-06-02 18:07:01,745 Created length plots
+2024-06-02 18:07:01,745 Created length plots
+2024-06-02 18:07:01,746 NanoPlot: Creating Read lengths vs Average read quality plots using 1000 reads.
+2024-06-02 18:07:01,746 NanoPlot: Creating Read lengths vs Average read quality plots using 1000 reads.
+2024-06-02 18:07:04,700 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/LengthvsQualityScatterPlot_dot  as png (or png for --legacy)
+2024-06-02 18:07:04,700 Created LengthvsQual plot
+2024-06-02 18:07:04,701 Writing html report.
+2024-06-02 18:07:04,701 Saved /home/bio.aau.dk/mk20aj/ONT-AmpSeq/.test/stats_out/stats/sample1/LengthvsQualityScatterPlot_dot  as png (or png for --legacy)
+2024-06-02 18:07:04,701 Created LengthvsQual plot
+2024-06-02 18:07:04,701 Writing html report.
+2024-06-02 18:07:04,754 Finished!
+2024-06-02 18:07:04,754 Finished!

.test/stats_out/stats/sample1/NanoStats.txt

@@ -0,0 +1,27 @@
+General summary:         
+Mean read length:              1,470.0
+Mean read quality:                20.2
+Median read length:            1,470.0
+Median read quality:              22.9
+Number of reads:               1,000.0
+Read length N50:               1,470.0
+STDEV read length:                14.9
+Total bases:               1,469,998.0
+Number, percentage and megabases of reads above quality cutoffs
+>Q5:	1000 (100.0%) 1.5Mb
+>Q7:	1000 (100.0%) 1.5Mb
+>Q10:	1000 (100.0%) 1.5Mb
+>Q12:	988 (98.8%) 1.5Mb
+>Q15:	958 (95.8%) 1.4Mb
+Top 5 highest mean basecall quality scores and their read lengths
+1:	31.5 (1472)
+2:	31.4 (1474)
+3:	30.9 (1472)
+4:	30.8 (1477)
+5:	30.7 (1474)
+Top 5 longest reads and their mean basecall quality score
+1:	1564 (13.9)
+2:	1511 (18.6)
+3:	1509 (24.6)
+4:	1507 (23.3)
+5:	1507 (24.1)

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