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
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.
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.