sophie-03 commented 3 years ago

Hi,

I am running Nucdiff on some data and I am getting the following error. I have run this exact script before on a different dataset which runs without any problem and I have doubled checked my filenames and format, could you please advise?

1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "/gpfs/ts0/projects/Undergraduate_Teaching-T109423/Synteny/gambusia_chr10/star10_gamb.ntref" of length 32921472

construct suffix tree for sequence of length 32921472

(maximum reference length is 536870908)

(maximum query length is 4294967295)

process 329214 characters per dot

....................................................................................................

CONSTRUCTIONTIME /gpfs/ts0/home/sm865/software/mummer/MUMmer3.23/mummer /gpfs/ts0/projects/Undergraduate_Teaching-T109423/Synteny/gambusia_chr10/star10_gamb.ntref 11.63

reading input file "/gpfs/ts0/projects/Undergraduate_Teaching-T109423/Gambusia/chr10a" of length 27243750

matching query-file "/gpfs/ts0/projects/Undergraduate_Teaching-T109423/Gambusia/chr10a"

against subject-file "/gpfs/ts0/projects/Undergraduate_Teaching-T109423/Synteny/gambusia_chr10/star10_gamb.ntref"

COMPLETETIME /gpfs/ts0/home/sm865/software/mummer/MUMmer3.23/mummer /gpfs/ts0/projects/Undergraduate_Teaching-T109423/Synteny/gambusia_chr10/star10_gamb.ntref 55.09

SPACE /gpfs/ts0/home/sm865/software/mummer/MUMmer3.23/mummer /gpfs/ts0/projects/Undergraduate_Teaching-T109423/Synteny/gambusia_chr10/star10_gamb.ntref 58.33

4: FINISHING DATA ERROR: Could not parse input from 'stdin'. Please check the filename and format, or file a bug report ERROR: postnuc returned non-zero

Could not run nucmer. Please, check nucmer input parameters values.

kseniakh commented 3 years ago

It seems that there is a problem with nucmer and not nucdiff. Can you run nucmer with this dataset?