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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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"ERROR ...: Problem running vsearch dereplication on file" #183

Open bk70545 opened 6 years ago

bk70545 commented 6 years ago

Hello When running the deblur workflow (deblur, version 1.0.4 as installed using the instructions on the code page), the pipeline fails at the dereplication step. Note that while I've attached the log file for a run where --trim-length was set to -1 (as my sequences were already trimmed to a uniform length), I have tried variations of this and the other options. deblur.log Here is an example of my header format: >C034x1070x23Feb2018x16SV34_1.

amnona commented 6 years ago

Hi,

  1. In the log file you attached, seems like the last deblur run failed since the output directory already exists. So maybe rerun deblur with the --overwrite flag?
  2. I see before that in the log an error with vsearch (just search for latest occurance of "vsearch" in the log file), but i didn't see any error output of vsearch. Can you try and run the vsearch command with the parameters detailed in the log file on the fasta file supplied to vsearch in the log file (if it isn't there, try running deblur with the --keep-tmp-files flag). Another possibility is that the input fasta file supplied to vsearch was empty/strange format. Can you look at that file and see what's in it?

Let me know how it goes Amnon

On Thu, Sep 6, 2018 at 3:18 AM bk70545 notifications@github.com wrote:

Hello When running the deblur workflow (deblur, version 1.0.4 as installed using the instructions on the code page), the pipeline fails at the dereplication step. Note that while I've attached the log file for a run where --trim-length was set to -1 (as my sequences were already trimmed to a uniform length), I have tried variations of this and the other options. deblur.log https://github.com/biocore/deblur/files/2354967/deblur.log Here is an example of my header format: >C034x1070x23Feb2018x16SV34_1.

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