collect() not working

5 views
Skip to first unread message

Jane

unread,
Nov 22, 2021, 6:34:15 AM11/22/21
to NGLess
Dear Luis,

Previously I was using ngless (v 1.1.1) and the collect function was working fine. Now that I am using a new cluster system, I had to install the new version of ngless (v 1.2). 
Using the same script, I get the following error message:

[Mon 22-11-2021 08:13:41]: The collect() call at line 43 could not be executed as there are partial results missing.
When you use the parallel module and the collect() function,
you typically need to run ngless *multiple times* (once per sample)!

And here's the script I used:

#!/usr/bin/env ngless
ngless "1.2"
import "parallel" version "1.0"
import "mocat" version "1.0"
import "motus" version "0.1"
import "igc" version "1.0"


samples = readlines('/scratch/e1376a01/healthy_data/04_list')
sample = lock1(samples)
input = load_mocat_sample(sample)

pd_mapped = map(input, reference='igc', mode_all=True)
pd_mapped_post = select(pd_mapped) using |mr|:
    mr = mr.filter(min_match_size=45, min_identity_pc=95, action={drop})
    if not mr.flag({mapped}):
        discard
        
counts_raw_KOs = count(pd_mapped_post, features=['KEGG_KOs'],normalization={raw}) 

collect(counts_raw_KOs, current=sample,allneeded=samples,ofile='pd_igc.KO_profiles.raw.tsv')

Could this be the issue with the new version?
By the way, I recently installed ngless using conda, however it was version 1.2 instead of 1.3.

Thank you.
Jane

Luis Pedro Coelho

unread,
Nov 22, 2021, 7:00:36 AM11/22/21
to Jane, NGLess List
Dear Jane,

I believe that the issue here is that by changing the version declaration line in your script, this invalidates the previous partial results, so you have to run everything anew.

Note that you can run older scripts with newer versions of NGLess (up to a point, but the software will give you an error message if you try to run very old versions).

So you can edit your script to state at the beginning

ngless "1.1"

and run it with software version 1.2 (it will run it in version 1.1 mode, but the changes are rarely very large)

Best
Luis


Luis Pedro Coelho | Fudan University | http://luispedro.org
--
You received this message because you are subscribed to the Google Groups "NGLess" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com.

Reply all
Reply to author
Forward
0 new messages