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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error at step 04.rundiamond.pl #643

Closed jahid10 closed 1 year ago

jahid10 commented 1 year ago

Hi, I was running SqueezeMeta in coassemly mode with the following command: home/bioinfo/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl -m coassembly -p metagenom_run_final -s /media/bioinfo/hdd2/final.samples -f /media/bioinfo/hdd1/Jahid_NGS_metagenomics/NGS_data_metagenomics --cleaning -c 300 --D --extdb /media/bioinfo/hdd2/Metagenome_jute/Cazy_db.list

during Step 4, I hit the following error, Can you please let me know why I encountered this particular error?

axaError running command: /home/bioinfo/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastp -q /media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final/results/03.metagenom_run_final.faa -p 12 -d /media/bioinfo/hdd1/Metagenome_databases/db/nr.dmnd -e 0.001 --id 40 -f tab -b 15.4 --quiet -o /media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final/intermediate/04.metagenom_run_final.nr.diamond at /home/bioinfo/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/04.rundiamond.pl line 72. Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally

Died at /home/bioinfo/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 1381.

syslog (1).zip

fpusan commented 1 year ago

Which version of SqueezeMeta are you using?

jahid10 commented 1 year ago

Hello, the version of SqueezeMeta im using is 1.5.1, Jan 2022

fpusan commented 1 year ago

This is most likely an issue that was fixed in 1.5.2. You can use the latest version of SqueezeMeta, or alternatively update SqueezeMeta's DIAMOND to 2.0.14 or higher

jahid10 commented 1 year ago

Thank you, but I haven't faced this issue in the previous run. The only different thing in this run is the inclusion of external database, everything else is similar, should I update SqueezeMeta to the latest version then?

fpusan commented 1 year ago

The issue only triggered for certain datasets and in certain platforms, so I would try updating first just to be sure

jtamames commented 1 year ago

In any case, could you paste your /media/bioinfo/hdd2/Metagenome_jute/Cazy_db.list file, just to verify it is fine?

jahid10 commented 1 year ago

Hi, sorry for the delay in response. It was solved after I correceted my db.list file and the rest of the run was went smoothly.