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taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
31 stars 6 forks source link

[BUG] Problem with kraken-type reports (from KrakenUniq) #123

Closed jfy133 closed 12 months ago

jfy133 commented 12 months ago

Is there an existing issue for this?

Problem description

We get the following error:

  [11:12:04] CRITICAL Error in sample 'ERR3201952.krakenuniq.report'  merge.py:424
                      with profile                                                
                      'ERR3201952.krakenuniq.report.txt'.                         
             CRITICAL   schema_context column             check       merge.py:427
                      check_number failure_case index                             
                      0         Column    dup  dtype('float64')                   
                      None        int64  None

Code sample

Run taxpasta 0.4.0 on the following file (entitled): ERR3201952.krakenuniq.report.txt

# KrakenUniq v1.0.2 DATE:2023-07-13T11:10:57Z DB:./testdb-krakenuniq DB_SIZE:358660 WD:/home/james/git/nf-core/taxprofiler/testing/blah/work/d4/9641b418650bf507e0b05143a5800d
# CL:/usr/local/bin/krakenuniq --db testdb-krakenuniq --threads 2 --report-file ERR3201952.krakenuniq.report.txt ERR3201952.merged.fastq.gz
%   reads   taxReads    kmers   dup cov taxID   rank    taxName
100 4937    4937    10648888    1   NA  0   no rank unclassified

ERR3201952.krakenuniq.report.txt

Environment

Anything else?

This is causing failures on the nf-core/taxprofiler dev branch

Midnighter commented 12 months ago

Damn, okay! Should be a quick fix.

jfy133 commented 12 months ago

:tada: it's currently blocking KU testing so that would be awesome :)