flass
commented
4 years ago Hi Laetitia,
back again! next game 🎾 :
Ok so there is an issue with detecting the 'locus_tag_prefix' column in your strain information file, which from the above seem to be this one usergenomeinfo=/scratch/clamchatka/Panta/user_genomes/strain_infos_test9.txt
From your previous error reports, I think the syntax for this file is correct... at least it seems to be !
here my guess is that you have manually written/edited this file under a non-Unix environment, and that the end-of-line feed is not the single \n character but something else (typically under Windows it is \r\n (see https://en.wikipedia.org/wiki/Newline).
The 'locus_tax_prefix' column being at the end of the line, that would explained why it's not recognised (because Python would read it as 'locus_tax_prefix\r'). I could code something that escapes this naughty character, but it is BAD in general to have the wrong EOL as many Unix-based programs just won't have it and make an error, so I won't encourage it.
It's easy to fix using the sed command.
And actually, I won't explain it here as this makes me think that I already explained that in another issue, cf. #14 ! So please refer to that one (and in the future have a look at previous issues before posting your own, it might have been resolved already 😉 )
Best,
Florent
megaptera-helvetiae
Hitting my next wall.
Tasks 0, 1, and 2 were error free. Task 3 completed with errors.
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