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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
53 stars 41 forks source link

error in trimming #51

Closed nclowell closed 4 years ago

nclowell commented 4 years ago

dDocent hit an error during trimming and I can't tell why.

Here's what's printed to the terminal:

/home/nclowell/miniconda2/envs/updated_dDocent/bin/dDocent: line 6: export: `2.7.8': not a valid identifier
dDocent 2.7.8 

Contact jpuritz@uri.edu with any problems 

Checking for required software

All required software is installed!

dDocent version 2.7.8 started Wed Sep 11 10:10:23 PDT 2019 

At this point, all configuration information has been entered and dDocent may take several hours to run.
It is recommended that you move this script to a background operation and disable terminal input and output.
All data and logfiles will still be recorded.
To do this:
Press control and Z simultaneously
Type 'bg' without the quotes and press enter
Type 'disown -h' again without the quotes and press enter

Now sit back, relax, and wait for your analysis to finish

Trimming reads
(updated_dDocent) nclowell@ubuntu:/mnt/hgfs/E/dDocent_configfile_test$

Here's the content of the trim log:

mawk: cannot open lengths.txt (No such file or directory) /home/nclowell/miniconda2/envs/updated_dDocent/bin/dDocent: line 688: / 2: syntax error: operand expected (error token is "/ 2")

nclowell commented 4 years ago

Oops! My bad. It looked like a trimming error but there was a mistake in one of the file names that didn't match the naming convention.