BLAT error while execution

Question

[amitpande74]

Hi, I installed BLAT locally using :

conda install -c bioconda blat

Then I ran BLAT with the following command:

blat /path/to/hg19.fa /dev/null /dev/null -makeOoc=/path/to/hg19.fa.11.ooc -repMatch=1024

When I run my fasta file it gives me an error:

blat /home/user/hg19.fa /home/user/Desktop/unaligned.fasta -ooc= /home/user/hg19.fa.11.ooc 
Loaded 3137161264 letters in 93 sequences
mustOpen: Can't open  to read: No such file or directory

Kindly guide. Thanks.

[GenoMax]

That is odd. I just tried the command and was able to generate .ooc file from a single multi-fasta human genome file. I don't know why you are getting following line?

blat /home/user/hg19.fa /home/user/Desktop/unaligned.fasta -ooc= /home/user/hg19.fa.11.ooc

I just got the following:

Loading /path_to/genome.fa
Counting /path_to/genome.fa
Writing 11.ooc
Wrote 32617 overused 11-mers to 11.ooc
Done making 11.ooc

[amitpande74]

Hi genomax, I just followed the instructions from this post: A: Is there a more efficient way of checking multiple sequences for how many hits t

What should be done to make a ooc file ? What was the command line you had used. Kindly help.

[GenoMax]

It was the same command as yours from original post. I assume the problem has been solved?

[amitpande74]

Got it genomax. Thanks.

[ATpoint]

The output message has a whitespace there, is this whitespace also in your input command?

[GenoMax]

That may be a red herring unless the original command had a space. We have no way to know.