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chrisquince / DESMAN

De novo Extraction of Strains from MetAgeNomes
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Error in pileups_to_freq_table.py, pileup file NOT FOUND #43

Open chiaramazzoni opened 4 years ago

chiaramazzoni commented 4 years ago

Hello, I'm running your desmanflow command and the following error occurs: DESMAN/scripts/pileups_to_freq_table.py assembly.fa *.pileup desmanfreqs.csv --> pileup_ins[f]=open(sys.argv[f+1]) FileNotFoundError: [Errno 2] No such file or directory: '*.pileup'. I looked into the work directories, and I guess it does not find the pileup because it is stored only in the previous wd and not copied in the next...still, coping it in the current wk and calling the original desmanflow command with -resume is does not help because a new wk without the pileup is created every time. Can you help? Thanks

koadman commented 4 years ago

Hi, what version of nextflow are you using, and are you able to share the input data? Newer nextflows introduced a new mechanism to collect files from multiple processes and I wonder if the approach taken in desmanflow.nf (written in 2016) has since broken somehow.

chiaramazzoni commented 4 years ago

My nextflow version is 19.10.0.5170..and sorry my co-assembly is too big to share :/

cyxamiy commented 2 years ago

Hello, I have the same problem as above. My nextflow version is 21.10.6 and I put my input data in https://github.com/cyxamiy/desman_testdata Could you help me to solve this problem? Thanks very much!

Hi, what version of nextflow are you using, and are you able to share the input data? Newer nextflows introduced a new mechanism to collect files from multiple processes and I wonder if the approach taken in desmanflow.nf (written in 2016) has since broken somehow.