Error: Database was built with a different version of Diamond and is incompatible.

[skrakau]

pipeline_report.txt
software_versions.csv

I don't know why, but I still get this error. [2021-05-07 14:21:46.114194] 47 bin(s) found!

Command error:
Error: Database was built with a different version of Diamond and is incompatib
le.
[2021-05-07 14:34:47.300571] ERROR: DIAMOND finished abnormally.

Work dir:
/ifs/groups/eces450650Grp/data/Assembly_Binning_old/work/81/95fee99d939f76a9ae3
1784c62007d

Tip: you can replicate the issue by changing to the process work dir and entering
the command bash .command.run

The workflow was completed at 2021-05-07T14:47:11.875034-
04:00 (duration: 1h 4m 7
s)

The command used to launch the workflow was as follows:

nextflow run nf-core/mag -resume -profile singularity --input 'CSJP002A_{R1,R2}
.fastq.gz' -c nextflow.config --max_memory 186.GB --max_cpus 20 --kraken2_db k2_p
luspf_20210127.tar.gz --cat_db CAT_prepare_20210107.tar.gz --outdir results_cat

Originally posted by @gailrosen in #74 (comment)

[skrakau]

Hi @gailrosen,

since you are using the latest release v1.2.0 and not the dev branch, the changes described in #74 do not yet apply for you (see also #90).

It seems the pre-build CAT database versions compatible with the Diamond version used in mag v1.2.0 are not available anymore on the CAT download site. That is not ideal for reproducibility, and we try to address this problem in future releases.

For now you could a) build it yourself with an compatible DIAMOND version (more complicated) or b) ask the CAT developers for a compatible database, e.g. "http://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20200304.tar.gz" (they provide it on request, easiest) or c) wait for the next mag release.

[gailrosen]

I still get the error when I try to use a different verison of DIAMOND. ./diamond --version
diamond version 2.0.6

And I put that diamond in the --path_to_diamond .... but it still gives the incompatibility flag. Shouldn't I be able to make it use the diamond that I put in that path? Or it's the fact that CAT is using a different version of DIAMOND?

[gailrosen]

[2021-05-19 10:31:17.324179] DIAMOND found: diamond version 0.9.24.

Ugh.. so it is finding an older DIAMOND.. where is it getting this from and why cannot i not overwrite it with --path_to_diamond ?

[skrakau]

One solution for such problems in the future is to create the CAT database yourself within the mag pipeline (--cat_db_generate), ensuring the same DIAMOND version for building the database and running the classification. See #196. Will be part of the next release.

[gailrosen]

Hi, It's unclear to me how to run --cat_db_generate. Do I put the path of the db I want to generate afterward? Should I still specify --cat_db? Can you give me an example of how to run this and where it saves the CAT db? thanks, Gail

…

________________________________________ From: Sabrina Krakau ***@***.***> Sent: Tuesday, May 25, 2021 6:35 AM To: nf-core/mag Cc: Rosen,Gail; Mention Subject: Re: [nf-core/mag] Error: Database was built with a different version of Diamond and is incompatible. (#188) External. One solution for such problems in the future is to create the CAT database yourself within the mag pipeline (--cat_db_generate), ensuring the same DIAMOND version for building the database and running the classification. See #196<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnf-core%2Fmag%2Fpull%2F196&data=04%7C01%7Cglr26%40drexel.edu%7C1bd47ce32c274fcfed7408d91f68c8bc%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575357184788372%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=YZ0i2Cjq928G%2FVdDHBrUQFZct57eITG3We66D9Xfmbc%3D&reserved=0>. Will be part of the next release. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnf-core%2Fmag%2Fissues%2F188%23issuecomment-847755518&data=04%7C01%7Cglr26%40drexel.edu%7C1bd47ce32c274fcfed7408d91f68c8bc%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575357184798371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wfZ4CQVHHh3iHjMDqJMjeK9U5AayrSH3AD0qicjc90Y%3D&reserved=0>, or unsubscribe<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABHZROPPJNBAXHUPIH7GQR3TPN4OFANCNFSM44N2QYBQ&data=04%7C01%7Cglr26%40drexel.edu%7C1bd47ce32c274fcfed7408d91f68c8bc%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575357184808367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eNIL%2B%2BT9KDtOtwuieVgipnqaOg3s4HlA1iFX6WhhBkE%3D&reserved=0>.

[skrakau]

No, --cat_db_generate and --cat_db are mutually exclusive. The parameter --cat_db_generate is a boolean parameter, thus it's sufficient to just specify this --cat_db_generate, maybe in combination with --save_cat_db . See #196.

However, note is only in the dev branch yet, release is in preparation.

[gailrosen]

ok thanks.

…

________________________________________ From: Sabrina Krakau ***@***.***> Sent: Tuesday, May 25, 2021 11:35 AM To: nf-core/mag Cc: Rosen,Gail; Mention Subject: Re: [nf-core/mag] Error: Database was built with a different version of Diamond and is incompatible. (#188) External. No, --cat_db_generate and --cat_db are mutually exclusive. The parameter --cat_db_generate is a boolean parameter, thus it's sufficient to just specify this --cat_db_generate, maybe in combination with --save_cat_db . See #196<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnf-core%2Fmag%2Fpull%2F196&data=04%7C01%7Cglr26%40drexel.edu%7C91748f7ed0544e2c7d2e08d91f92ad24%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575537096783245%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=oVL%2BZqYJorH9TAT0cUG%2FeI6Kcy0%2Bd8tEE0iidhS%2BuNw%3D&reserved=0>. However, note is only in the dev branch yet, release is in preparation. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnf-core%2Fmag%2Fissues%2F188%23issuecomment-847975890&data=04%7C01%7Cglr26%40drexel.edu%7C91748f7ed0544e2c7d2e08d91f92ad24%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575537096783245%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jHlKVQm5WYYs2bqJo5FsJa3fQWr6N66f9LHrUudq4yE%3D&reserved=0>, or unsubscribe<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABHZROPECCJF7623EHPJ5MDTPO7SXANCNFSM44N2QYBQ&data=04%7C01%7Cglr26%40drexel.edu%7C91748f7ed0544e2c7d2e08d91f92ad24%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C637575537096793237%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tVh3yfLXSzYQ3yTuJChnOB9uIC2ciAGdXdoszdy2o14%3D&reserved=0>.