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hsgweon / pipits

Automated pipeline for analyses of fungal ITS from the Illumina
GNU General Public License v3.0
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error non zero returncode re-inflating sequences. #35

Closed peernils closed 4 years ago

peernils commented 4 years ago

Dear all,

I also encountered the non-zero returncode error but in a different part of the pipeline, during the re-inflating sequences. After the pipits-funits command. I have tried the suggestions made in earlier threads but it still gave me the error. If somebody has some suggestions that would be appreciated.

(pipits_env) henriks-mini:pipits_test henrik$ pipits_funits -i out_seqprep/prepped.fasta -o out_funits -x ITS2 pipits_funits 2.4, the PIPITS Project https://github.com/hsgweon/pipits

2019-11-28 10:16:41 pipits_funits started 2019-11-28 10:16:41 Checking input FASTA for illegal characters 2019-11-28 10:16:41 ... done 2019-11-28 10:16:41 Counting input sequences 2019-11-28 10:16:41 ... number of input sequences: 53 2019-11-28 10:16:41 Dereplicating sequences for efficiency 2019-11-28 10:16:41 ... done 2019-11-28 10:16:41 Counting dereplicated sequences 2019-11-28 10:16:41 ... number of dereplicated sequences: 20 2019-11-28 10:16:41 Extracting ITS2 from sequences [ITSx] 2019-11-28 10:16:44 ... done 2019-11-28 10:16:44 Counting ITS sequences (dereplicated) 2019-11-28 10:16:44 ... number of ITS sequences (dereplicated): 19 2019-11-28 10:16:44 Sorting by ID 2019-11-28 10:16:44 ... done 2019-11-28 10:16:44 Removing short sequences below < 100bp 2019-11-28 10:16:44 ... done 2019-11-28 10:16:44 Counting length-filtered sequences (dereplicated) 2019-11-28 10:16:44 ... number of length-filtered sequences (dereplicated): 19 2019-11-28 10:16:44 Re-inflating sequences 2019-11-28 10:16:44 Error: None zero returncode: python /Users/henrik/miniconda2/envs/pipits_env/bin/pipits_rereplicate -i out_funits/intermediate/derep.ITS2.sizefiltered.fasta -o out_funits/ITS.fasta --uc out_funits/intermediate/derep.uc (pipits_env) henriks-mini:pipits_test henrik$

hsgweon commented 4 years ago

So first thing - can you check your python version? It should be Python 3.

So in pipits_env:

source activate pipits_env
python --version

Can you let me know the output?

hsgweon commented 4 years ago

I have just noticed that you have installed miniconda2. Can you possibly try PIPITS on miniconda3?