search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
348 stars 81 forks source link

01.run_all_assemblies.pl. #683

Closed aalkin2001 closed 1 year ago

aalkin2001 commented 1 year ago

Hi, I got this error message when analyzing microbiome data from ONT: Assembly not present in /PATH/01.micr_analysis_out.fasta. I realize that the micr_analysis_out.contigs.fasta required for the next step wasn't generated. Please have a look at the attached syslog for possible advice on how to resolve this issue. I am running the Squeezemeta tool with biconda on a cluster. syslog.zip

jtamames commented 1 year ago

Hello All seems correct, but indeed the assembly was not generated. Could you check if Flye produces any output? Just add-a flye to your command line

aalkin2001 commented 1 year ago

Yes, I also used flye, and I still got the same error message. So I've attached the syslog for flye.

syslog.zip

aalkin2001 commented 1 year ago

Hi, To follow up on the above-submitted issue. Would you happen to know why I am getting the error and what is the possible solution?

Thanks

fpusan commented 1 year ago

It looks like a problem with your system libraries. What is your OS and version?

aalkin2001 commented 1 year ago

I've attached a screenshot of the OS and version.

OS version

Thanks.

fpusan commented 1 year ago

I see, you are on RHEL and we have not tested SQM there. It works in CentOS7 so I would have expected it to work there too, but apparently some binaries don't... Anyways you'll likely need to download flye, compile it in your machine, and then make SQM use that new version. I can help you with the last part, but not with the others...

El jue., 11 may. 2023 16:46, aalkin2001 @.***> escribió:

I've attached a screenshot of the OS and version.

[image: OS version] https://user-images.githubusercontent.com/30750268/237724855-b67b6250-f0cd-46d9-a0a3-a9f4cc0d4292.png

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/683#issuecomment-1544121495, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACAHO7SQYWO7RXNW77FV2VDXFT3STANCNFSM6AAAAAAX3NSBLU . You are receiving this because you commented.Message ID: @.***>

aalkin2001 commented 1 year ago

Thank you for the suggestions. I have been able to resolve the issue.