# Long running time with the --bypass-prescreen mode

**URL:** <https://forum.biobakery.org/t/long-running-time-with-the-bypass-prescreen-mode/2209>\
**Category:** HUMAnN\
**Created:** [June 7, 2021, 3:32am UTC](https://forum.biobakery.org/t/long-running-time-with-the-bypass-prescreen-mode/2209 "2021-06-07T03:32:25Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ruizzhan](https://avatars.discourse-cdn.com/v4/letter/r/e79b87/32.png) [@ruizzhan](https://forum.biobakery.org/u/ruizzhan)\
**Post date:** [June 7, 2021, 3:32am UTC](https://forum.biobakery.org/t/long-running-time-with-the-bypass-prescreen-mode/2209/1 "2021-06-07T03:32:25Z")

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Hello everyone,

I am interested in knowing the functional potential of the microbial communities in some soil metagenomic samples. After following the standard pipeline of HUMAnN3, I obtained some decent results regarding pathways and gene families. However, the relative abundance of unmapped results seems to be pretty high with roughly 93%. Therefore, I thought I might be able to improve the mapping rate by skipping the taxonomic profiling step using the **–bypass-prescreen** flag.

HUMAnN3 did not complete the task in 3 days by utilizing 187G of memory (48 cores) on a university HPC when I turn on the **—bypass-prescreen** flag on a sample with a size of ~15GB (obtained by merging 150bp paired end reads). The process took 16 hours with the same setting without —bypass-prescreen.

So my questions here are:

1. Am I using the —bypass-prescreen function for the right purpose, can I actually improve the mapping rate with it?
2. I am expecting it to take much longer since it will utilize the whole Chocophlan DB. Can I get any perspective as to how much longer is it going to take?
3. The job stopped running after 3 days, I’d like to get it running again using - **-resume** , but it didn’t work, is there a compatibility issue when you have both —resume and —bypass-prescreen?

Any insight would be much appreciated!

Best,  
Rui

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [June 9, 2021, 7:48pm UTC](https://forum.biobakery.org/t/long-running-time-with-the-bypass-prescreen-mode/2209/2 "2021-06-09T19:48:41Z")

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`--bypass-prescreen` will index the entire ChocoPhlAn database for a really broad nucleotide-level search, which is not usually the best course (the option is mostly there for testing purposes). For a soil sample I’d recommend switching to the UniRef50 database, which will allow HUMAnN to pursue more relaxed mapping during the translated search phase (thus increasing your unclassified mapping rate).

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**Author:** ![ruizzhan](https://avatars.discourse-cdn.com/v4/letter/r/e79b87/32.png) [@ruizzhan](https://forum.biobakery.org/u/ruizzhan)\
**Post date:** [June 10, 2021, 2:26am UTC](https://forum.biobakery.org/t/long-running-time-with-the-bypass-prescreen-mode/2209/3 "2021-06-10T02:26:23Z")

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Thank you for your advice, I will give it a try!