No dbCAN HMM database found

[JoelPHoward]

Hello,

I installed saccharis_2 on an HPC cluster using conda. The version I am running is 2.0.0.dev22.

I am trying to test saccharis using the following command:

saccharis \
--family GH43 \
--subfamily 1 \
--cazyme_mode all_cazymes \
--domain bacteria \
--seqfile sequences.faa \
--verbose \
--threads 10 \
--tree fasttree

But while dbcan is running, I get the following error:

*********************************************
* Appending user sequences takes:
*        0.1 seconds to run
*********************************************
dbCAN processing of GH43_1_ALL_CAZYMES_cazy_UserFile00000.fasta is underway...
ERROR: No dbCAN HMM database found.         Please make sure that your dbCAN HMM database is named 'dbCAN-HMMdb-V8.txt' or the newest one, has been through hmmpress, and is located in your database directory

I manually downloaded dbCAN-HMMdb-V8.txt from dbcan and tried rerunning before and after passing it through hmmpress, but I still experience the same error.

Any suggestions?

[AlexSCFraser]

Some questions to help me:

What version of dbcan is installed?

Did you install the python packages using in a conda env, in a pyenv, or just bare pip install?

Could you list the contents of the saccharis db directory?

I know another use had an issue on a cluster because their home directory was limited in size and a temporary solution was to use symlinks to respect the limited home drive size but still point to the correct files. Is there any limitations on filesizes in your home directory?

[JoelPHoward]

Hi Alex,

The version of dbcan is 3.0.7. I used conda env to install enverything.

./saccharis/
├── config
│   └── advanced_settings.json
├── db
│   ├── CAZy.dmnd
│   ├── dbCAN-HMMdb-V12.txt
│   ├── dbCAN-HMMdb-V12.txt.h3f
│   ├── dbCAN-HMMdb-V12.txt.h3i
│   ├── dbCAN-HMMdb-V12.txt.h3m
│   ├── dbCAN-HMMdb-V12.txt.h3p
│   ├── dbCAN-HMMdb-V8.txt
│   ├── dbCAN-HMMdb-V8.txt.h3f
│   ├── dbCAN-HMMdb-V8.txt.h3i
│   ├── dbCAN-HMMdb-V8.txt.h3m
│   ├── dbCAN-HMMdb-V8.txt.h3p
│   ├── dbCAN-PUL_07-01-2022.txt
│   ├── dbCAN-PUL_07-01-2022.xlsx
│   ├── dbCAN-PUL.tar.gz
│   ├── dbCAN_sub.hmm.h3f
│   ├── dbCAN_sub.hmm.h3i
│   ├── dbCAN_sub.hmm.h3m
│   ├── dbCAN_sub.hmm.h3p
│   ├── dbCAN.txt.h3f
│   ├── dbCAN.txt.h3i
│   ├── dbCAN.txt.h3m
│   ├── dbCAN.txt.h3p
│   ├── fam-substrate-mapping-08252022.tsv
│   ├── PUL.faa
│   ├── PUL.faa.pdb
│   ├── PUL.faa.phr
│   ├── PUL.faa.pin
│   ├── PUL.faa.pjs
│   ├── PUL.faa.pot
│   ├── PUL.faa.psq
│   ├── PUL.faa.ptf
│   ├── PUL.faa.pto
│   ├── stp.hmm.h3f
│   ├── stp.hmm.h3i
│   ├── stp.hmm.h3m
│   ├── stp.hmm.h3p
│   ├── tcdb.dmnd
│   ├── tf-1.hmm.h3f
│   ├── tf-1.hmm.h3i
│   ├── tf-1.hmm.h3m
│   ├── tf-1.hmm.h3p
│   ├── tf-2.hmm.h3f
│   ├── tf-2.hmm.h3i
│   ├── tf-2.hmm.h3m
│   └── tf-2.hmm.h3p
└── logs
    └── cli_logs.txt

Note the dbCAN-HMMdb-V8 and dbCAN-HMMdb-V12 files were manually downloaded after I experienced the error. Since I was able to download these files manually, I don't think it is a file size issue. I also checked my storage allocation in my home directory and it should be more than enough.

Since posting this issue, I tried to run saccharis on my personal computer (Macbook pro, 13-inch 2020, OSX 12.6.3), but experienced the exact same error. The HPC is linux based.

[lowkri]

Hi Joel. Sorry for the delayed response.

If you download the dbCAN-HMMdb-V12.txt and then rename to dbCAN.txt, it should work after this point.

I'll work on getting a fix pushed out.

[jzrapp]

Hi,

I am getting the same error. dbCAN processing of GH34_ALL_CAZYMES_cazy_UserFile00000.fasta is underway... ERROR: No dbCAN HMM database found. Please make sure that your dbCAN HMM database is named 'dbCAN-HMMdb-V8.txt' or the newest one, has been through hmmpress, and is located in your database directory

My db folder contains CAZy.dmnd dbCAN-PUL_07-01-2022.txt dbCAN-PUL_07-01-2022.xlsx dbCAN-PUL.tar.gz dbCAN_sub.hmm.h3f dbCAN_sub.hmm.h3i dbCAN_sub.hmm.h3m dbCAN_sub.hmm.h3p dbCAN.txt.h3f dbCAN.txt.h3i dbCAN.txt.h3m dbCAN.txt.h3p fam-substrate-mapping-08252022.tsv PUL.faa PUL.faa.pdb PUL.faa.phr PUL.faa.pin PUL.faa.pjs PUL.faa.pot PUL.faa.psq PUL.faa.ptf PUL.faa.pto stp.hmm.h3f stp.hmm.h3i stp.hmm.h3m stp.hmm.h3p tcdb.dmnd tf-1.hmm.h3f tf-1.hmm.h3i tf-1.hmm.h3m tf-1.hmm.h3p tf-2.hmm.h3f tf-2.hmm.h3i tf-2.hmm.h3m tf-2.hmm.h3p

How can I work around it? Thanks!

[lowkri]

Hi. It seems you're missing the dbCAN.txt. Please go to dbCAN's website and download the latest database version: https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V12.txt

This file should be renamed to dbCAN.txt and put in your ~/saccharis/db folder.

The current version of SACCHARIS on GitHub has this and a few other bugs patched, but we're working on uploading it to bioconda still.