Inchworm process fails

[sergiogonmoll]

Hi Clem,

I'm trying to run dnaPipeTE on fastq.gz files with trimmed and post-QC reads and it seems to work fine until the Inchworm bit of the Trinity run, where it gives me this message:

If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

I think it's strange because I'm running it interactively in a cluster with massive storage space. The error keeps occuring even when decreasing the genome coverage to 0.01. What could be going wrong? Thank you in advance for your help!

[clemgoub]

Hi Sergio!

The most likely cause could be that your interactive allocation has less than 10Gb or RAM, which is the minimum required to run inchworm (jellyfish actually, to get the k-mers). This is definitely a RAM issue, not a storage problem. Are you using the container version?

Let me know if increasing the RAM works, otherwise, send me the full log and command you used, we'll find a fix!

Cheers,

Clément

[sergiogonmoll]

Hi Clément,

I tried increasing the RAM allocation, but the job would still crash. I resorted to lowering the coverage, but increasing the number of samples (i.e. 5 samples of 0.1 coverage instead of 2 samples for 0.25 coverage). This stabilized the run and I managed to have them finish. Probably there is a limitation on samples size when running Trinity? I think I would consider the issue solved. Thank you!

Cheers,

Sergio

[clemgoub]

Hello Sergio,

Thanks for the feedback, and I'm happy you found a solution that works. Before I close the thread, would you mind sharing the sample size that worked in reads/bp (as well as the amount that didn't)? Though 0.25X is usually fine, if it's a big genome that can be a lot?

Still I'm surprised that Trinity would not handle it -- so I'd like to keep an eye on that! Thanks again for reporting! It helps a lot!

Cheers,

Clément

[sergiogonmoll]

Hi Clément,

Yes, the genome size is 1091184475 bp. I thought so too. We just transitioned to a new cluster and it's turning out to be quite temperamental, so maybe it has something to do with that? Best of luck!

Cheers,

Sergio