Maybe a bug: Linked source for ....not found

[depengl]

Hello,
I have been using this command for a long time, it woks well at HaMStR v.13.2.10. I installed HaMStR v.13.2.11 by ' conda install -c bionf hamstr' in a new system and then met this error. Is this a bug?
I am using a core_ortholog set trained by ourselves. Since input files are protein sequences, there are only *_prot.fa in blastdir. It seems that this hamstr doesn't recognize option "-protein".
Thank you!

command:
hamstr -hmmset=arthNreg2 -protein -cleartmp -cpu 12 -central -strict -refspec=drome_4 -sequence_file=Paranesidea_sp_croco.fas -taxon=Paranesidea_sp -representative
error:
checking for reference fasta files: Linked source for /home/depengli/HaMStR/blast_dir/drome_4/drome_4.fa not found in /mnt/d/Croco_hamstr_workdir! at /home/depengli/HaMStR/bin/hamstr line 1172.

[trvinh]

Hi @depengl ,
I am currently on vacation, cannot check it on the computer. However, I suggest that you should try: remove the option -protein; and in the blast_dir, use *.fa instead of *_prot.fa (make sure that the blast db files are built using this *.fa, not *_prot.fa)
I hope that will work again :-)
P.S.: Please excuse me if I do not reply immediately. If in case you still have problems, Ingo @ebersber will be back from vacation on 10.08, he can help you to look at the code.

[depengl]

Hi @depengl ,
I am currently on vacation, cannot check it on the computer. However, I suggest that you should try: remove the option -protein; and in the blast_dir, use *.fa instead of *_prot.fa (make sure that the blast db files are built using this *.fa, not *_prot.fa)
I hope that will work again :-)
P.S.: Please excuse me if I do not reply immediately. If in case you still have problems, Ingo @ebersber will be back from vacation on 10.08, he can help you to look at the code.

Thank you!
The same ortholog-set has been always working well before this HaMStR version. I can understand, if the new version no longer support the old core ortholog set.
Have a good vacation!

Depeng