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biocore / deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
BSD 3-Clause "New" or "Revised" License
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Errors: IndexError: index returns 3-dim structure and ERROR: `3` is not supported in --blast [STRING]. #150

Closed smteo closed 7 years ago

smteo commented 7 years ago

Hi,

I'm trying Deblur for the first time and ran the following command: deblur workflow --seqs-fp seqs.fna --output-dir deblur_test -t 240 --min-reads 1 --min-size 1 --keep-tmp-files --log-level 1

It returned with an error: File "/usr/local/easybuild/software/Python/3.5.2-vlsci_intel-2015.08.25/lib/python3.5/site-packages/scipy/sparse/sputils.py", line 344, in _index_to_arrays raise IndexError('index returns 3-dim structure') IndexError: index returns 3-dim structure

When I look in the log file the are these errors: ERROR(47590929782720)2017-05-02 12:54:32,325:sortmerna error on file /vlsci/SG0006/shared/COAST_16S/AGRF_CAGRF13540_002/flash_output/split_lib_output/deblur_tes t/deblur_working_dir/53_AULMM_AATCAGTCTCGTL001.extendedFrags.fastq.fasta.trim.derep ERROR(47590929782720)2017-05-02 12:54:32,325:stdout : ERROR(47590929782720)2017-05-02 12:54:32,325:stderr : ERROR: 3 is not supported in --blast [STRING].

amnona commented 7 years ago

It seems maybe you have the wrong sortmerna version installed in the deblur conda environment? Can you source activate the deblur environment and type: sortmerna --version It should be SortMeRNA version 2.0, 29/11/2014

smteo commented 7 years ago

My version now is 2.1. I will install 2.0 and try again. Thank you.

wasade commented 7 years ago

@smteo, is this still an issue? Please reopen if necessary.