Comments (3)
from hamstr.
i add a new species use the command "addTaxon1s -f genome/2019_043_Pni.pep.filter.fa -i 13216 -o /data/01/user102/orthology/hamstr -c --force", there is no error on runing;
from hamstr.
Hi @hhy18
first of all, as stated in the README of this repo, HaMStR (or hamstr1s) is dead and has been replaced by fDOG.
Secondly, for your issue, my best guess is that you are using a human seed protein with a non-human reference species (158543 is the ID for a plant, if I am correct). So, it can cause the problem for the (re-)blast search, that the seed sequence could not be found. If you want to test it, you can take any sequence from your ARIFI@158543@1 species as the seed protein and run HaMStR again with that sequence. The reference species for HaMStR should always be the species where you get the seed sequence from.
However, I really recommend you change this tool to fDOG, because we are not supporting HaMStR any longer :-)
Regards,
Vinh
from hamstr.
Related Issues (20)
- check existing annotation before calculating FAS
- FAS: Input HOT 1
- data redundancy and unused script(s) HOT 1
- potential of using out-dated data/tools HOT 1
- move related documents (posters) to gh-pages
- long-format for phyloprofile input HOT 2
- Error running sample file HOT 10
- CAST not working HOT 8
- oneSeq not working HOT 2
- Problem during annotation HOT 2
- For loop not working HOT 1
- clean up result files (data package), set new checksum
- Maybe a bug: Linked source for ....not found HOT 2
- auto deploying to pypi
- accelerated mode
- scoreThreshold
- temporary FAS input files
- update pfam db (30.0 -> 32.0)
- hmmsearch ranking
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from hamstr.