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GenomiqueENS / toulligQC

A post sequencing QC tool for Oxford Nanopore sequencers
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Run toulligQC error #3

Closed gligong closed 5 years ago

gligong commented 6 years ago

Ok, I tried our barcoded nanopore data, and toulligqc generated reports. So, for non bar coded data, what can I do because tougligqc requires sample sheet file?

It gives KeyError: 'sample_sheet_file' Thanks!

George

I am trying to run toulligQC to generate albacore run reports. I tried different options, and always got errors. It looks like that toulligqc requires all the options even when the run does not have barcodes. I ran following cammand: toulligqc -n test_run \ -f /storage/FILES/Oxford_Minion/Hudson_Sept8_FLO-MIN106_SQK-LSK108/Sept_R9.4_flowcells/testReport/0 \ -a /storage/FILES/Oxford_Minion/Hudson_Sept8_FLO-MIN106_SQK-LSK108/Sept_R9.4_flowcells/testReport/ \ -q /storage/FILES/Oxford_Minion/Hudson_Sept8_FLO-MIN106_SQK-LSK108/Sept_R9.4_flowcells/testReport/fastq \ -o /storage/FILES/Oxford_Minion/Hudson_Sept8_FLO-MIN106_SQK-LSK108/Sept_R9.4_flowcells/testReport/report and got following errors: Traceback (most recent call last): File "/home/apps/toulligQC/toulligQC-20170912/bin/toulligqc", line 11, in load_entry_point('toulligqc===-0.1a1-', 'console_scripts', 'toulligqc')() File "/home/apps/toulligQC/toulligQC-20170912/lib/python3.6/site-packages/toulligqc-0.1a1-py3.6.egg/toulligqc/toulligqc.py", line 229, in main check_conf(config_dictionary) File "/home/apps/toulligQC/toulligQC-20170912/lib/python3.6/site-packages/toulligqc-0.1a1-py3.6.egg/toulligqc/toulligqc.py", line 142, in check_conf if not config_dictionary['sample_sheet_file']: File "/home/apps/toulligQC/toulligQC-20170912/lib/python3.6/site-packages/toulligqc-0.1a1-py3.6.egg/toulligqc/toulligqc_conf.py", line 46, in getitem return self._config_dictionary[item] KeyError: 'sample_sheet_file'

I am wondering if you could show me how to run toulligqc with following output from an Albacore run. The pass directory has 0, 1, 2 sub directories holding fast5 files. Fastq files are also in the pass directory. Thanks!

George

albacoreResults\ ----- configuration.cfg ----- pipeline.log ----- sequencing_summary.txt ----- workspace\ ------ fail\ ------ pass\ --------- 0\ --------- 1\ --------- 2\ --------- fastq_runid_31ee3c191ce764f50a56b1bbee67326bf4c6d40e_0.fastq --------- fastq_runid_31ee3c191ce764f50a56b1bbee67326bf4c6d40e_1.fastq --------- fastq_runid_77317b2780c17bc6d729717e91f58ff31823c8a8_2.fastq

jourdren commented 6 years ago

Hi,

I've just fixed the issue (barcoding option was always on) with the "8377072" commit. Please update your ToulligQC Git repository with a git fetch origin master && git pull and then reinstall ToulligQC.

Best regards,

Laurent.