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 (?)