No output files #56
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Hi abcbot123 :) Thanks for reaching out. At a first glance, the problem originates within i-ADHoRe, while the other warnings in the later commands arise from the fact that some orthologs Ks data are still not generated (probably interrupted by the error?). The i-ADHoRe error message says: It's thus related to line 95 in file Profile.cpp. It seems to me that i-ADHoRe is not finding the data it expects to find. Could you double check if your GFF file follows the standard format and could you make sure you're parsing it with the correct gff_feature and gff_attribute? Cheers, |
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Here's an update :) If the above is correct, then you should still be able to run ksrates using the whole-paranome pipeline, deactivating the colinearity pipeline (see configuration). Best, |
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Hi :) It would also probably still be helpful if you could provide us with your input FASTA and GFF files for Oxalis, as well as with the parsing gff_features and gff_attribute you have chosen. Thanks! |
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Hi Cecilia, |
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Hi, I'm happy it was just a format issue! Feel free to share what it was if you think other people might encounter the same problem. |
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Hi Cecilia, |
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Hi, I'm having a similar problem, here's the code to run and the errors reported, can you help me see how to fix it? ksrates plot-paralogs config_Bchinensis.txt INFO Generating mixed paralog and ortholog distributions There is also an error in the above step ksrates orthologs-analysis config_Bchinensis.txt INFO Computing ortholog distribution peaks with related error INFO Loading parameters and input files |
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Hi wjq1981, Thanks for reaching out! The error originating from command The output from command Let me know how it goes, and if this doesn't help we can investigate further! |
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Thank you for your prompt reply. ksrates plot-paralogs config_elaeis.txt |
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This is a list of all the files in the “paralog_distributions” directory. paralog_distributions/wgd_elaeis Wouldn't 'elaeis.ks.tsv' be 'elaeis.ks_anchors.tsv' here either? Because it's the first time I've run it and I don't know what their contents should be! |
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Alright! In the docs you can find the description of the output files: for example here it explains that The directory structure can tell us something: normally |
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This is the output log. ksrates paralogs-ks config_elaeis.txt --n-threads=64 INFO - - - - - - - - - - - - - - - - - - - - - Process 1/1 is alive on suma-Nd. ************* i-ADHoRe parameters ************* Creating dataset... done. (time: 0.132908s) All Done! Bye... |
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Based on the output log, i-ADHoRe was doing alright until the very end: it printed "All Done! Bye..." and then something generated an error with message "Authorization required, but no authorization protocol specified". For example, here the problem was that the user was running commands as "root" and not as "user": https://www.reddit.com/r/linux4noobs/comments/lu1plx/hi_i_get_this_authorization_required_but_no/ and https://stackoverflow.com/questions/48833451/no-protocol-specified-when-running-a-sudo-su-app-on-ubuntu-linux |
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Thank you very much for your answer. docker run --rm -v $PWD:/temp -w /temp vibpsb/ksrates -h |
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Let's see, here in the docs I showed how to use the docker commands, and it looks like you chose the one to "launch a single command through the container": |
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Yeah, you're right. Now that it's working with “ksrates”, I'm crying at my own stupidity. Good day！ |
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No worries, great to hear this worked! Should you find an answer for the authorization-related error, let me know :) |
Hi,
I'm using the ksrates docker image. I have an issue with not getting relevant output files. Here are the codes I have run,
When I check the errors, this is what I found this error related to i-adhore step,
Here are the other errors and warnings I got,
Do you have any suggestions to fix this error?
Thanks so much!
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