Stopping in STEP4

[RIJP-SU]

Hi, I am new to SqueezeMeta. I just successfully passed test_install.pl and run with test files. But I got following error at STEP4, any solution would be aprreciate. My version of SqueezeMeta is 1.6.2post2. Additinally, I found Spades assembly is not working in this version. It seems version of spades is too old as the newest spades in my naitive envirionment worked fine.

Working with taxonomy database in /path/to/db/nr.dmnd taxaError running command: /path/to/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastp -q /path/to/test/Hadza/results/03.Hadza.faa -p 35 -d /path/to/db/nr.dmnd -e 0.001 --id 40 -f tab -b 126 -o /path/to/test/Hadza/intermediate/04.Hadza.nr.diamond > /path/to/test/Hadza/temp/diamond.nr.log 2>&1 at /path/to/envs/SqueezeMeta/SqueezeMeta/scripts/04.rundiamond.pl line 77. Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /path/to/test/Hadza/syslog file (zip it first) Died at /path/to/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941.

[jtamames]

Hello It is likely that the databases are not properly installed. Did you download them and run the test_install.pl script? Best, J

[fpusan]

Can reproduce the error with spades. Also can you share with us the /path/to/test/Hadza/temp/diamond.nr.log and /path/to/test/Hadza/syslog files?

[RIJP-SU]

Thanks jtamaes for your quick response, I have run the test_install.pl and got "All checks successful".

Thanks fpusan for your quick response, I am attaching two log files. diamond.nr.log syslog.zip

[fpusan]

It seems DIAMOND was killed a few moments after beginning. Why did you set -b to 126? This is a too high value which can potentially draw lots of memory (hence the process being killed). Also is this running locally or on a computing cluster?

[RIJP-SU]

Thanks fpusan, I am running locally. No paticular reasons for setting -b to 126, just thought higher would be faster. What is proper number? Is default fine?

[fpusan]

Yes, by default we will dynamically set -b based on your available memory, capping it to a reasonable value. You can edit the /path/to/test/Hadza/SqueezeMeta_conf.pl file and modify the $blocksize variable so the line reads like $blocksize = NF; Then restart the project.

[RIJP-SU]

Thanks fpusan, I'll try accordingly. Will share the result later.

[RIJP-SU]

BTW, are you able to fix the things about Spades sooner or later?

[fpusan]

I'm testing the fix right now, SPAdes seems to be running ok, I will make the release once I check it finishes correctly

[RIJP-SU]

Thanks fpusan, as I'm planning to process short reads, I would like to have Spades as an option!

[fpusan]

Megahit (our default) is comparable to SPAdes for short reads processing. But yes, I will most likely release the fix in a few hours

[RIJP-SU]

Hi, after adjusting the parameter for $blocksize, STEP4 have finished without errors, now moved to STEP5. Thanks for your swift solution! Looking forward to the update of Spades fixed version!

[fpusan]

The issue with SPAdes has been fixed in 2fbf69d and released in a new version of SqueezeMeta (v1.6.2post3)