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Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
GNU Affero General Public License v3.0
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Error "hmmsearch: not found ... local variable 'hmmout' referenced before assignment" while running FeGenie #29

Open anapopov opened 3 years ago

anapopov commented 3 years ago

Hi, I'm interested in identifying iron related genes within a metatranscriptomics dataset. I have attempted providing a fasta with gene (nucleotide) or protein sequences as bellow, but I hit an error that says hmm not found. Please see below.

Thanks! Ana~

command: FeGenie.py -bin_dir ORFs/ -bin_ext fasta -out TEST_out --orfs

All required arguments provided!

HMM AsbE_petrobactin_synthesis-rep Cyc1 Cyc2_repCluster1 . . . GACE_1846 GACE_1847 nramp zip starting main pipeline...

2 Looking for following iron-related functional category: iron_storage sh: 1: hmmsearch: not foundta: 33%
rm: cannot remove 'TEST_out/test_proteins.fasta-HMM/Transferrin_TbpB_binding_protein_Haemophilus_influenzae_P44971.hmm.txt': No such file or directory FeGenie cannot find the correct hmmsearch output files. If you provided gene or ORF-call sequences, please be sure to specify this in the command using the '--orfs' flag Traceback (most recent call last): File "/home/.../FeGenie/FeGenie.py", line 3083, in main() File "/home/.../FeGenie/FeGenie.py", line 821, in main for line in hmmout: UnboundLocalError: local variable 'hmmout' referenced before assignment

Arkadiy-Garber commented 3 years ago

Hi Ana,

Thanks for your interest in FeGenie! Sorry that you are getting errors, but hopefully we can get to the bottom of what's causing this.

Could you tell me how you installed FeGenie?

Also, FeGenie does not accept nucleotide gene sequences. It will take protein sequences, but ideally, you should provide contigs if you can.

Thanks! Arkadiy

anapopov commented 3 years ago

Thanks for your quick response Arkadiy!

I don't have conda, so I installed it within my vbox Ubuntu as per the alternative instructions:

git clone https://github.com/Arkadiy-Garber/FeGenie.git cd FeGenie bash setup.sh

I added it to my path, and had to install r and prodigal also.

re: prodigal/contigs - I get the same error using the test run provided:

... Looking for following iron-related functional category: iron_storage sh: 1: hmmsearch: not foundctinomycetemcomitans.txt: 33%
rm: cannot remove 'fegenie_out/Aggregatibacter_actinomycetemcomitans.txt-HMM/Transferrin_TbpB_binding_protein_Haemophilus_influenzae_P44971.hmm.txt': No such file or directory

Arkadiy-Garber commented 3 years ago

Hi Ana,

Based on what I can see from that error message, it looks like HMMER is not installed on your system (hmmsearch is the main command that FeGenie uses from the HMMER package). Here's a full list of dependencies that FeGenie requires: https://github.com/Arkadiy-Garber/FeGenie/wiki/Installation. However, I would highly recommend installing Conda. It will make installation of FeGenie (and countless other programs) much easier. I can't count how many hours of needless installation Conda has saved me.

anapopov commented 3 years ago

Oops - I totally missed that. Likely because I previously had it installed. Thanks Arkadiy!

I'll try the contigs too. Very interested to see what we can dig up in this data. Re: Conda - noted!

Arkadiy-Garber commented 3 years ago

Sounds good! Yes, I hope FeGenie helps you uncover some interesting iron genes! Let me know if you continue to have any issues.

Thanks, Arkadiy