Question: FastQ Screen "no BWA index was found"
0
gravatar for KaiserinLissi
7 months ago by
KaiserinLissi0 wrote:

Hi, I´m very new to all the NGS processing stuff, but I installed fastq screen successfully and indexed 3 genomes using BWA (human, E. Coli and a custom made one). So far everything went well, but when I try to run fastq screen it gives me this error;

Using '/home/usr/Software/fastq_screen_v0.13.0/bwa/bwa' as BWA path
Skipping DATABASE 'Human' since no BWA index was found at '/home/usr/Genomes/Homo_sapiens/GRCh38_genomic.fa.sa'

despite the path in the config file should be the right one, and I can´t see what else could be the problem (obviously there are all files which should be produced by the bwa index command).

This is the path in the config file for the human genome;

/home/usr/Genomes/Homo_sapiens/GRCh38_genomic

Maybe any of you knows how I could solve this problem?

bwa fastq screen • 364 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by KaiserinLissi0
1

FastQ screen is looking for bwa indexes in /home/franziskasafi/Genomes/Homo_sapiens/ directory. Where as you appear to refer to a different directory in config file (not sure what that config is for). Either move/soft link your bwa index files in the directory where FastQ screen is looking for indexes.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax70k

I´m sorry, I forgot to edit the path in the first hand (because of names). It is all the same path.

Yes, this is how my config-file looks like and the files that are inside of the folders of the indexed genomes.

ADD REPLYlink modified 7 months ago • written 7 months ago by KaiserinLissi0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Then based on @Vijay's answer the config file path should include names of the directory along with the fasta file.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax70k

Ok, I found the problem. Vijay pointed me to the soultion; You need to use the fasta file which you indesed, but not the other files made while indexing. Thank you everbody for your hints :)

ADD REPLYlink written 7 months ago by KaiserinLissi0
1

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 7 months ago by genomax70k
2
gravatar for lakhujanivijay
7 months ago by
lakhujanivijay4.2k
India
lakhujanivijay4.2k wrote:

Say if you are working with test.fasta and that you have provided the following in the config file

## trial1
DATABASE        trial1       /path/test.fasta

then, your path should be the absolute location of the the .fasta file along with the index files like this.

test.fasta
test.fasta.amb
test.fasta.ann
test.fasta.bwt
test.fasta.pac
test.fasta.sa
ADD COMMENTlink written 7 months ago by lakhujanivijay4.2k

Ok, I found the problem. Vijay pointed me to the soultion; You need to use the fasta file which you indesed, but not the other files made while indexing. Thank you everbody for your hints :)

ADD REPLYlink written 7 months ago by KaiserinLissi0
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