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khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics
http://www.recentrifuge.org
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min() arg is an empty sequence [error] #29

Closed JChristopherEllis closed 3 years ago

JChristopherEllis commented 3 years ago

Hi,

I tried to run recentrifuge after reinstalling and got the following error. How can I resolve this problem?

Thanks, Chris

$ rcf -n /nfs/data/bsd/je0/taxdump -k /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/ -c 2 -o /nfs/data/bsd/je0/schadt/recentrifuge/trimmed/all_quality_trimmed_seqs.html -s KRAKEN -y 25

=-= /nfs/data/bsd/je0/miniconda3/bin/rcf =-= v0.28.14 - December 2019 =-= by Jose Manuel Martí =-=

Kraken .krk files to analyze: ['/nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P1-S1.krk', '/nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P2-S2.krk'] Control(s) sample(s) for subtractions: /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P1-S1.krk /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P2-S2.krk Loading NCBI nodes... OK! Loading NCBI names... OK! Building dict of parent to children taxa... OK!

Please, wait, processing files in parallel...

Loading output file /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P1-S1.krk... OK! Seqs read: 11_788 [5.41 Mnt] Seqs clas: 2_197 (81.36% unclassified) Seqs pass: 48 (97.82% rejected) Scores SHEL: min = 102.0, max = 589.0, avr = 197.6 Coverage(%): min = 26.3, max = 100.0, avr = 47.8 Read length: min = 261 nt, max = 783 nt, avr = 364 nt TaxIds: by classifier = 529, by filter = 22 Building from raw data with mintaxa = 2 ... Check for more seqs lost ([in/ex]clude affects)... OK! /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P1-S1 ctrl OK! Load elapsed time: 0.114 sec

Loading output file /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P2-S2.krk... OK! Seqs read: 11_915 [5.45 Mnt] Seqs clas: 2_241 (81.19% unclassified) Seqs pass: 52 (97.68% rejected) Scores SHEL: min = 97.0, max = 623.0, avr = 232.1 Coverage(%): min = 25.0, max = 100.0, avr = 57.8 Read length: min = 266 nt, max = 622 nt, avr = 365 nt TaxIds: by classifier = 545, by filter = 20 Building from raw data with mintaxa = 2 ... Check for more seqs lost ([in/ex]clude affects)... OK! /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/P2-S2 ctrl OK! Load elapsed time: 0.125 sec

Please, wait. Performing cross analysis in parallel...

multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/nfs/data/bsd/je0/miniconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/nfs/data/bsd/je0/miniconda3/lib/python3.8/site-packages/recentrifuge/core.py", line 393, in process_rank shared_analysis() File "/nfs/data/bsd/je0/miniconda3/lib/python3.8/site-packages/recentrifuge/core.py", line 172, in shared_analysis min_taxa=get_shared_mintaxa(), File "/nfs/data/bsd/je0/miniconda3/lib/python3.8/site-packages/recentrifuge/core.py", line 72, in get_shared_mintaxa return min([mintaxas[smpl] for smpl in raws[controls:]]) ValueError: min() arg is an empty sequence """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/nfs/data/bsd/je0/miniconda3/bin/rcf", line 813, in main() File "/nfs/data/bsd/je0/miniconda3/bin/rcf", line 782, in main analyze_samples() File "/nfs/data/bsd/je0/miniconda3/bin/rcf", line 495, in analyze_samples [r.get() for r in async_results]): File "/nfs/data/bsd/je0/miniconda3/bin/rcf", line 495, in [r.get() for r in async_results]): File "/nfs/data/bsd/je0/miniconda3/lib/python3.8/multiprocessing/pool.py", line 768, in get raise self._value ValueError: min() arg is an empty sequence

khyox commented 3 years ago

Chris, thanks for the issue report here!

I would say that the problem could be related to a very low number of reads passing the filters (you can see a rejection rate close to 98% in the output) but I don't see any non-control sample beyond the 2 control samples, which does not make sense.

So, please:

  1. Update Recentrifuge to the last release since you are using a quite old (beta) version.
  2. After the update, if you try again and see the same or a similar problem, please fill the standard form for issues that provides the essential information to look into the problem. I pasted it below for your convenience:

Bug report

Bug summary

Running Recentrifuge

Command line

$ rcf -n /nfs/data/bsd/je0/taxdump -k /nfs/data/bsd/je0/schadt/kraken2/trimmed/all_krk/ -c 2 -o /nfs/data/bsd/je0/schadt/recentrifuge/trimmed/all_quality_trimmed_seqs.html -s KRAKEN -y 25

Data

Actual outcome

# If applicable, paste the console output here
#
#

Expected outcome

Versions

JChristopherEllis commented 3 years ago

Hi Jose,

I installed this two days ago with conda... conda install -c bioconda recentrifuge

Is there a newer conda install version?

Thanks, Chris

JChristopherEllis commented 3 years ago

Quick update. uninstalled and reinstalled again. I now have new version.

Reran and had no issues. Thanks for your help Jose!

khyox commented 3 years ago

Thanks for the update, Chris! I am glad it is working now. Enjoy!