blast could not create a unit counts container

Question

I build a blast local database. However, when I run the blastn command I got this error message:

T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_250088_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1448906370/c++/compilers/unix/../../src/algo/winmask/seq_masker_istat_factory.cpp", line 170: Error: ncbi::CSeqMaskerIstatFactory::DiscoverStatType() - could not open

T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_250088_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1448906370/c++/compilers/unix/../../src/algo/winmask/seq_masker_istat_factory.cpp", line 271: Error: ncbi::CSeqMaskerIstatFactory::create() - could not create a unit counts container

I am using this command to create the blast local database:

makeblastdb -in chr23.fa -parse_seqids -dbtype nucl 

And this is my command for executing the blastn:

blastn -task megablast -db HumanGenome/blastdb/chr23.fa -window_masker_taxid 9606 -query readBatch.txt -out blastOut.txt

Any help would be really appreciated..thanks

Answer 1

Appears that you need to create the WindowMasker files first:

https://www.ncbi.nlm.nih.gov/books/NBK279687/

Specifically, linked content mentioned Step 1:

https://www.ncbi.nlm.nih.gov/books/NBK279681/#cookbook.Create_masking_information_usin_1

Answer 2

If windowmasker isn't an absolute requirement, consider RepeatMasker

There's multiple installation steps, but thy're all pretty straightforward. I find their documentation better than the windowmasker documentation, and they claim better masking coverage.

(My experience is specifically with the free HMMER/Dfam option.)

(I second Vince's remarks about the requirement for creating a masking database... have you tried running the same blastn without the windowmasker option?)