Kneaddata- any options to checkpoint the runs and resume the runs

Infrastructure and utilities KneadData
1

Dear Kneaddata developers,

I am running kneaddata 0.7.3 for my microbiome analysis of pair end reads

I have an unusual large file to run through kneaddata. I am wondering if the program can be check point or restarted at various junctions. My network is unable to support prolonged walltime at such high computing memory and they have advised me to breakdown my jobs.

My command was

[$PATH] kneaddata --input XXX_1P.fq.gz --input XXX_2P.fq.gz -db Database --output XXX --bypass-trim

The files size were 16.8gb and 19.8gb and that is causing a lot of issue on memory and walltime requirements.

I have already run trimmomatic separately/

Thank you.

Yik Weng

2

Hi Yik Weng, Sorry we don’t have an option to stop/restart kneaddata in the middle of processing. We do have options to bypass steps like trimmomatic so if you have already run that step you could run kneaddata with the bypass flag so it does not run it again (like you have in your command).

There is an option to use multiple threads which should speed up your runs you might try adding --threads N.

Thank you,
Lauren

3

Dear Lauren,

Your suggestion to use multiple thread works very well and helped us to solve our problem.

Sincerely grateful.

Thank you!!

Yik Weng

4

Glad to hear it worked!

Thanks!
Lauren