Roary error message : MSG: Got a sequence without letters. Could not guess alphabet
Hello i'm using roary for pan genome analysis for 22 strains fir i annotated the fasta files ( that i downloaded from ncbi ) of these strains and used gff files as input for roary , everything works fine till :
kraken-report: database ("/lustre/scratch118/infgen/pathogen/pathpipe/kraken/minikraken_20140330/") does not contain necessary file database.kdb kraken-report: database ("/lustre/scratch118/infgen/pathogen/pathpipe/kraken/minikraken_20140330/") does not contain necessary file database.kdb Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 141 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 142 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 143 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 144 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 145 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Use of uninitialized value in require at /home/manouar/miniconda3/envs/Obitools/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.
Saving 7 x 7 in image
Warning messages:
1: Removed 4 row(s) containing missing values (geom_path).
2: Removed 4 row(s) containing missing values (geom_path).
Saving 7 x 7 in image
Use of uninitialized value in require at (eval 767) line 1.
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
DOI https://doi.org/10.5281/zenodo.1146014
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 146 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
And here's the summary files Core genes (99% <= strains <= 100%) 0 Soft core genes (95% <= strains < 99%) 3 Shell genes (15% <= strains < 95%) 2034 Cloud genes (0% <= strains < 15%) 10828 Total genes (0% <= strains <= 100%) 12865
looking on this results seesms like some files "dosen't belong to the strains " but i'm quiet sure that all the strains belong to the same species , any solution please to solve this error , and also how can i know the files that cause this error Thank you
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For the future, if you post messages then please remove irrelevant sections as these parallel log messages. Running
parallel --citationjust once would save you from all that spam.I think you need to check your input files to be 100% sure there are no empty files or files missing sequences (check especially if you have multi genbanks).
Thank you for your reply , i don't have any emty file , can you tell me how can i know if have multigenbanks , just to be sure
Grep a file for the "LOCUS" line. If there is more than one, its a multi genbank, and you may have an entry without any sequence.
Thank you , i did it but i didn't find anything abnormal