01.run_all_assemblies.pl.

[aalkin2001]

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]

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]

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

syslog.zip

[aalkin2001]

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]

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

[aalkin2001]

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

Thanks.

[fpusan]

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 <#683 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACAHO7SQYWO7RXNW77FV2VDXFT3STANCNFSM6AAAAAAX3NSBLU> . You are receiving this because you commented.Message ID: ***@***.***>

[aalkin2001]

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