Assembly error in seqmerge mode

[matevzl533]

Hi,

I am trying to process 24 metagenomes (150PE) and was trying to run seqmerge mode. I get this error after it has finished processing individual files: STEP1 -> MERGING ASSEMBLIES: 01.merge_sequential.pl Starting assembly merge Error running command: /home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/kmerdist.pl /home/matevz/noccaea_seqmerge 1 >> /home/matevz/noccaea_seqmerge/syslog 2>&1 at /home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/01.merge_sequential.pl line 55. Stopping in STEP1 -> 01.merge_sequential.pl. Program finished abnormally Died at /home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/01.run_all_assemblies.pl line 233. Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

/home/matevz/noccaea_seqmerge is my project folder for SqueezeMeta. The syslog file is attached. Any help would be greatly appreciated.

Best,

Matevz syslog.zip

[fpusan]

Try running the following command LD_LIBRARY_PATH=/home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/lib /home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/kmer-db build -t 12 /home/matevz/noccaea_seqmerge/temp/samples.noccaea_seqmerge.txt /home/matevz/noccaea_seqmerge/temp/kmerdb.noccaea_seqmerge.txt -k 12 -f 1 and let us know the output (should be an error)

[matevzl533]

After the above command, I get this: `Kmer-db version 1.7.2 (15.01.2020) S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Illegal instruction (core dumped)`

[fpusan]

What is your OS?

[matevzl533]

I am running Ubuntu 22.04.2 LTS.

[fpusan]

Hi again! Can you download kmer-db from https://github.com/refresh-bio/kmer-db, compile it and then use the resulting binary to replace the executable at /home/matevz/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/kmer-db?

[matevzl533]

Hi, this seemed to work. Now it has progressed pass the point of the previous error. Thank you very much for your help.

[fpusan]

Glad to hear! Closing issue

[fpusan]

Actually reopening as I realized I need to provide a permanent fix for this, hopefully soon

[fpusan]

Hopefully fixed in aa8d4d6

[rakeshkrpatra]

Hi, this seemed to work. Now it has progressed pass the point of the previous error. Thank you very much for your help.

Please can you elaborate how do you do that download and compilation? please

[fpusan]

You should download the source code from https://github.com/refresh-bio/kmer-db Then you should compile it manually. How to do it will depend a bit on your platform, but normally what works is to go to the directory with the source code and type make. Then you should copy the executable to the right directory. In the latest SqueezeMeta version this would be /path/to/conda/envs/SqueezeMeta/bin