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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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rename: not enough arguments #27

Open dieunelderilus opened 2 years ago

dieunelderilus commented 2 years ago

I am trying to run decona in 2 barcoded folders (barcode01/ and barcode02/), after concatenating and and filtering , the program stops running and prints the message bellow. Not that the recommendations provided in issue #7 do not not solve the problem.

(decona) [qlk5@biolinux new]$ decona -f -l 400 -m 1000 -q 10 -c 0.80 -n 100 -M Filtering data barcode01_concatenated.fastq... Filtering data barcode02_concatenated.fastq... Data filtered with NanoFilt Data not demultiplexed Fastq reads are being transformed to fasta rename: not enough arguments

Usage: rename [options] expression replacement file...

Options: -v, --verbose explain what is being done -s, --symlink act on symlink target

-h, --help display this help and exit -V, --version output version information and exit

For more details see rename(1).

Any help please? Cheers, ~DD

AlexGaithuma commented 2 years ago

This solves it

 conda install -c bioconda rename -y
dieunelderilus commented 2 years ago

I have done this , but unfortunately this doesn't solve it. The problem looks to be not the installation of 'rename' itself, but the argument provided in the code. Any other alternative? I am having this problem even with test dataset you have provided.

Cheers, ~DD

AlexGaithuma commented 2 years ago

Try the solution: https://github.com/Saskia-Oosterbroek/decona/issues/7#issuecomment-953087933

dieunelderilus commented 2 years ago

As I stated in my first post, unfortunately the recommendation provided in # (comments) did not solve this problem.

AlexGaithuma commented 2 years ago

Try to Edit the file in decona/bin/decona.yml add the line

dependencies:
  - rename=1.600

Then delete the decona environment and create it again. Should work!

dieunelderilus commented 2 years ago

Thank you very much Alex , adding the 'rename' dependency makes it work as perfectly!

Cheers, ~DD