Nucmer_and_ABACAS

[pari_89]

Hi everyone,

I have been using ABACAS in order to map contigs to a reference genome and all the contigs from mira, ray, newbler, cap3 seem to run and produce results except for CLCworkbench contigs file

I am getting this error:

# CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 1.14
# reading input file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta" of length 2814092
# matching query-file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta"
# against subject-file "nucmer.ntref"
# COMPLETETIME /usr/bin/mummer nucmer.ntref 5.95
# SPACE /usr/bin/mummer nucmer.ntref 5.65
4: FINISHING DATA
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero
Use of uninitialized value in addition (+) at abacas.1.3.1.pl line 1001.
Total contigs = 0
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1013.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1014.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1015.


I am pretty sure, my file is in the correct format because I have used it with other software before.

So if anyone could please help me?

Thank you.

[A.N.Other]

I am pretty sure, my file is in the correct format because I have used it with other software before.

Have you actually checked to ensure the format of the input fasta file? Have a 5sec visual inspection of it with a viewer like less.

[pari_89]

Have you actually checked to ensure the format of the input fasta file? Have a 5sec visual inspection of it with a viewer like less.

Yes, I confirm it is in fasta file format and I have used it with other software before and it worked fine. Is there any other reason why it cannot align it??

Thank you.

[A.N.Other]

It's a pretty cryptic error message, and I haven't come across it myself. Things you might look into:

Was the file generated on a unix system? -- I'm thinking windows \r\n linebreaks (as opposed to \n on unix systems), though I don't know if it would make a difference here?

Spaces in the FASTA file headers? - some programs don't like them. Again, I'm not sure about nucmer, as my automated workflows have _ instead of spaces to avoid things like this.

[pari_89]

Spaces in the FASTA file headers? - some programs don't like them

Yes, I am using Biolinux as platform. I have also changed the headers to Contig1 and simplified them but still no luck.

[muol]

Abacas' blind spot is show-tiling from mummer, and I guess your nucmer.tiling file is empty, causing this Perl error. It happens if show-tiling cannot stitch together the consensus from nucmer.delta. I recommend to run mummer directly and optimize parameters.

[pari_89]

Abacas' blind spot is show-tiling from mummer, and I guess your nucmer.tiling file is empty, causing this Perl error. It happens if show-tiling cannot stitch together the consensus from nucmer.delta. I recommend to run mummer directly and optimize parameters.

Hi, I fixed the problem. Actually, the FASTA file was exported on a windows platform and I was running mummer on linux. I just copied the fasta file contents in a linux editor. It parsed the file correctly.

Thanks

Hope this helps someone.