Two problems with QfO2011

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So i have 2 problems with the 2011 QfO dataset. After downloading the fasta files, i renamed all such that there are no .faa in the name and no '.' Then i run sonicparanoid -t 64 -i input/ -o output/

and i get the following error :

(...)
Predicting 2145 ortholog tables...ERROR: The alignment file for 43-19 was not found, please generate alignments first
.ERROR: the alignment file (/local/3024874.1.parallel_long/output/alignments/43-19) was not found, it is required to perform orthology inference.
ERROR: The alignment file for 43-51 was not found, please generate alignments first
.ERROR: the alignment file (/local/3024874.1.parallel_long/output/alignments/43-51) was not found, it is required to perform orthology inference.

ERROR: the ortholog relationship file for the pair 19-43 was not found!

Ortholog tables creation elapsed time (seconds):        136.701
(...)

(repeated 2 times)

using only 16 cores, i get a different error:

(...)
/home/admin/sonicparanoid/lib/python3.6/site-packages/sonicparanoid/orthogroups.py:318: RuntimeWarning: invalid value encountered in true_divide
  seedRatioArr = (geneCntArr - inparaCntArr)/geneCntArr
Ortholog tables loaded for multi-species orthology:     2145

Creating ortholog groups...
(...)

i use python-3.6.4.

not sure which version i have (i installed with http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/ yesterday) sonicparanoid --help says its version 1.0 but the bin/sonicparanoid file containes a version number 1.1.1 (?)

Comments (1)

  1. Salvatore Cosentino

    Hello, and thank you for your message.
    From version 1.1.1 you do not need to rename the FASTA files anymore.

    I am investigating the problem about the missing alignments, it seems it happens on some systems, and I am also havong that problem recently.

    The version should be shown correctly from version 1.1.2

    Also please note that the source code has moved to GitLab
    https://gitlab.com/salvo981/sonicparanoid2

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