Java Error

[thomlmarshall]

Hi Remi,
I've been trying to run MitoFinder on a dataset of 34 whole genome files and I'm running into some issues. I'm running this on a cluster using LAUNCHER to run in parallel, and I seem to be alternating between two errors: I'm either getting 1.) ERROR: java is not installed/loaded., and 2.) ERROR: MEGAHIT didn't run well
Please check log file : /scratch/05104/thomm/22111Hil_N22089/22111Hil_H21189_S187_L004/megahit.log
Launcher: Job 11 completed in 597 seconds.
Launcher: Task 92 done. Exiting.

I assumed the second to be an issue with memory allocation, but I'm puzzled with the first error. I have java downloaded in my mitofinder environment. I've also tried loading the cluster's java module. The thing that really confuses me is that I am not getting this error consistently, but every time I think I might have the memory issue solved, I'm hit with the Java error again. Perhaps this is an issue I should take up with my cluster's IT department, but just wanted to see if you had any suggestions.

Thanks!
Thom

[RemiAllio]

Hi Thom,

Thank you for your message.

Since the error seems to be a dependency issue, I was wondering if you could use the singularity container of MitoFinder?
It would be the easiest way to solve the problem in my opinion.

Best,
Rémi

[thomlmarshall]

Thanks for the suggestion, this worked!

Thom

[RemiAllio]

Nice! Thank you for your feedback 🙂
Best,
Rémi

[thomlmarshall]

Hi Remi, As soon as I said this, I began having some issues again unfortunately. I have some larger files of samples that were sequenced to high coverage (each sample has paired end reads with about 250 M reads each), and I can't seem to get Mitofinder to run on them. I've tried submitting them together and individually, with each sample using an entire node (128 cores each). My results have ranged from the Java error popping up again (saying that Java is not installed or loaded) to no output at all (not even error or output files). Are these files simply too large? Let me know if you have any ideas! Thanks so much for your help. Thom

…

On Thu, Jun 23, 2022 at 3:04 PM Rémi Allio ***@***.***> wrote: Nice! Thank you for your feedback 🙂 Best, Rémi — Reply to this email directly, view it on GitHub <#35 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALXWOYHSCTLMHBFUXR7DVMLVQS7NPANCNFSM5ZOMT54Q> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

-- *Thomas L. Marshall, MS* PhD Candidate, Hillis lab Department of Integrative Biology University of Texas at Austin

[RemiAllio]

Hi Thom,

Ok, I am sorry but I don't know what is is going on with your cluster and I am afraid you will have to check with your cluster's IT department since it seems to be quite specific.

Otherwise, is there anything written in the MitoFinder logs (e.g. megahit.log)?

Finally, regarding the possible memory issue, you don't need to use all your reads to run MitoFinder. You can start using ~20M reads per sample and see if that's enough to assemble the mitogenome. If not, you can then add more reads and try again but we usually assemble complete mitogenomes with less than that (from WGS data).

Sorry for the inconvenience,
Best,
Rémi

[thomlmarshall]

Hi Remi, Thank you for the reply. I'm now attempting to run MitoFinder using singularity. The job is still running but it's showing the following error in the error file: ERROR: ld.so: object '/opt/apps/xalt/xalt/lib64/libxalt_init.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. I'm not sure what this means, but is this something that will prevent the job from running correctly? Thanks! Thom

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On Wed, Jun 22, 2022 at 2:36 AM Rémi Allio ***@***.***> wrote: Hi Thom, Thank you for your message. Since the error seems to be a dependency issue, I was wondering if you could use the singularity container of MitoFinder <https://github.com/RemiAllio/MitoFinder#run-mitofinder-with-singularity>? It would be the easiest way to solve the problem in my opinion. Best, Rémi — Reply to this email directly, view it on GitHub <#35 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALXWOYARMGXYRA4S2APPCTLVQK66DANCNFSM5ZOMT54Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Thomas L. Marshall, MS* PhD Candidate, Hillis lab Department of Integrative Biology University of Texas at Austin

[RemiAllio]

Hi Thom,

Since the error seems to be ignored, let's let it finish and see what happens!
Fingers crossed!

Cheers,
Rémi