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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Error in { : task 1 failed - "object 'contig' not found" #36

Closed aerijman closed 2 years ago

aerijman commented 2 years ago

Dear Alan,

preprocess worked but difference is throwing the error described in the title.

This is the command:

nanodisco difference -nj 4 -nc 1 -p 1 -f 10 -l 11 -i analysis/preprocessed_subset -o analysis/difference_subset -w b24 -n b23 -r reference/mergenome.fasta

And this is the standard output: ''' Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete local:2/0/100%/0.0s Error in { : task 1 failed - "object 'contig' not found" Calls: %do% -> Execution halted local:1/1/100%/127.0s Error in { : task 1 failed - "object 'contig' not found" Calls: %do% -> Execution halted local:0/2/100%/63.5s '''

I am looking forward to getting your help to solve this issue. Thank you!

touala commented 2 years ago

Hello @aerijman,

Were you able to diagnose the issue already? From this error message, I don't know what is the underlying issue. Early on, I encounter issue when contig names were only numerical (">1209" instead of ">contig_1209"), so maybe this is similar.

Do any output files are generated? Alternatively, you could try to run a command with likely less ressources:

nanodisco difference -nj 1 -nc 1 -p 1 -f 10 -l 10 ...

Best,

Alan

touala commented 2 years ago

Hello @aerijman,

Feel free to reopen if the issue is not sorted.

Best,

Alan