BLAT error while execution
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12 months ago
amitpande74 ▴ 20

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 • 359 views
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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

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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.

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

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Got it genomax. Thanks.

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

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