Question: BLAT error while execution
0
gravatar for amitpande74
7 months ago by
amitpande740 wrote:

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.

blat error • 238 views
ADD COMMENTlink modified 7 months ago by ATpoint41k • written 7 months ago by amitpande740

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
ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

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.

ADD REPLYlink written 7 months ago by amitpande740
1

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

ADD REPLYlink written 7 months ago by genomax92k

Got it genomax. Thanks.

ADD REPLYlink written 7 months ago by amitpande740

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

enter image description here

ADD REPLYlink written 7 months ago by ATpoint41k

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

ADD REPLYlink written 7 months ago by genomax92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1879 users visited in the last hour