Single copy gene prediction using diamond failed. Aborting

[bhimbbiswa]

Hi.

I am doing metagenomic analysis in Atlas (https://github.com/metagenome-atlas/atlas) pipeline.

I am getting this error again and again. Please help to solve.

DAS Tool run on  Wed Dec 9 10:47:40 JST 2020

User environment details:
Rscript path:  /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/bin/Rscript
Rscript version:  R scripting front-end version 4.0.3 (2020-10-10)
pullseq path:  /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/bin/pullseq
pullseq version:  Version: 1.0.2 Name lookup method: UTHASH
prodigal path:  /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/bin/prodigal
prodigal version:  Prodigal V2.6.3: February, 2016
ruby path:  /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/bin/ruby
ruby version: 
diamond path:  /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/bin/diamond
diamond version:  diamond version 2.0.5

Running DAS Tool using 1 thread.
identifying single copy genes using diamond version 2.0.5

single copy gene prediction using diamond failed. Aborting

I tried increasing the ram as well as changing the number of threads but same problem.

It stops with a core dump. core.25573.txt

Please find the required logs attached. DASTool.log Main_log.txt S13_DASTool.log

[cmks]

Can you check if ruby is installed on your system? According to your log file, an executable with the name 'ruby' seems to exist but it's interesting that it does not return the version information. Try to run:

ruby --version

The output should be something like:

ruby 2.5.1p57 (2018-03-29 revision 63029) [x86_64-linux-gnu]

[bhimbbiswa]

Hi.

Thank you very much for your reply.

It shows

ruby 2.7.2p137 (2020-10-01 revision 5445e04352) [x86_64-linux]

I again updated ATLAS and again ran the analysis. But same error. Please find the logs attached below. DASTool.log S13_DASTool.log Atlas_all.sh.e11245365.txt

As ATLAS create its own conda environment, please find a copy of JSON file attached about Ruby.

Ruby_JSON_copy.txt

I think this problem is similar to #5 #11 #13 and #48 as I got similar output in(see DASTool.log)

I dearly wanted to use DASTool for my analysis. Can you please help me. Regards,

Bhim

[cmks]

Hi Bhim,

Thanks for your log files and environment information. Your ruby looks fine to me. Can run the single copy gene prediction script directly using the following command and see if there are any error messages (you may have to adjust some paths)?

./DAS_Tool/src/scg_blank_diamond.rb diamond S13/annotation/predicted_genes/S13.faa DAS_Tool/db/bac.all.faa DAS_Tool/db/bac.scg.faa DAS_Tool/db/bac.scg.lookup 1

While running some tests, I've noticed that diamond has an issue with writing temporary files when the database is located on a mounted volume. I'm not sure if that's the problem in your case. However, the error message looks like this:

Searching alignments... Device not configured
Device not configured
Error: Error writing file diamond-tmp-2RAS0b Error: Error writing file diamond-tmp-nH2nTe

libc++abi.dylib: terminating with uncaught exception of type File_write_exception: Error writing file diamond-tmp-nH2nTe
libc++abi.dylib: terminating with uncaught exception of type File_write_exception: Error writing file diamond-tmp-2RAS0b

Cheers, Chris

[bhimbbiswa]

Hi.

I am really sorry for my very late reply. Was stuck in some other work.

I used the following command but again core dump happened.

/lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/src/scg_blank_diamond.rb diamond /lustre7/home/bhimbiswa/New_micro/S13/annotation/predicted_genes/S13.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.all.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.scg.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.scg.lookup 1

This is the output I got

/var/spool/uge/m06/job_scripts/11282269: line 8: 63698 Segmentation fault      (core dumped) /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/src/scg_blank_diamond.rb diamond /lustre7/home/bhimbiswa/New_micro/S13/annotation/predicted_genes/S13.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.all.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.scg.faa /lustre7/home/bhimbiswa/New_micro/databases/conda_envs/92a32d4b/share/das_tool-1.1.2-1/db/bac.scg.lookup 1

DAStool.sh.txt

Reagrds,

Bhim

[bhimbbiswa]

As suggested by @yanhui09 in #13, removing Ruby from my conda environment solved the problem.

As suggested, I used the following command in the conda environment in which this program was running.

conda remove ruby --force

Closing this issue as the problem is solved.