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bioinfo-ut / PlasmidSeeker

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
BSD 3-Clause "New" or "Revised" License
36 stars 11 forks source link

Error: Creating the wordmap failed! Died at plasmidseeker.pl line 156 #25

Closed ABMolBio closed 2 years ago

ABMolBio commented 2 years ago

Hi, during plasmid_seeker run, I am having this error again and again -

Loading database... Converting sample reads to k-mers... Finding coverage of bacterial isolate... gt4_wordmap_new: could not mmap file ./16442730219721tmp_closest_32.list Error: Creating the wordmap failed! Died at plasmidseeker.pl line 156.** I have tried with different reference sequence downloaded from NCBI Refseq. It worked with only one, but with others, its showing this error. How can I correct it ? Can you help me with this ?

bioinfo-ut commented 2 years ago

glistcompare has problems running in your system or with your files. Test whether you can normally execute binaries that are located in your GenomeTester4/ folder.

bioinfo-ut commented 2 years ago

Also, check whether you have provided all input files and in the correct format.

ABMolBio commented 2 years ago

Hey,

I already tested the GenomeTester4 binaries while running the example script. Moreover, the script is running successfully with one specific ref genome. But when I am changing the reference genome, it is showing this error. I tried with 3-4 different reference genomes. I rechecked, my reads and reference files are in correct fastq and fasta format. What should I do ?

bioinfo-ut commented 2 years ago

If it runs with one reference genome, then the software seems to work normally. The problem should be in the input files. Try to find the differences between working and non-working input files that may cause the error. We cannot help you without having your input files.

bala-ruokavirasto commented 2 years ago

Hi,

For future reference, Kindly Unzip the input file genome solved this error for me.

Bala