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

[bk70545]

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]

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 ***@***.***> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#183>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFkA8uAIrabhwm78FYlFud390yOI9JRYks5uYGm-gaJpZM4Wb5Sx> .