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-   -   Bowtie2 Exited with a Value of 1 (http://seqanswers.com/forums/showthread.php?t=59586)

Milestailsprowe 06-08-2015 11:49 PM

Bowtie2 Exited with a Value of 1
 
Hello I'm trying to align a bowtie2 index file with a fasta file. No matter what I do it ends with value of 1. How do I stop this?

http://i.imgur.com/Om0Rscm.jpg

dpryan 06-09-2015 12:08 AM

Try building the index for "genome.fa" first:

Code:

bowtie2-build genome.fa genome
Then "-x genome" would be the proper method to specify where the indices are (from your current path at least).

Milestailsprowe 06-09-2015 12:19 AM

Quote:

Originally Posted by dpryan (Post 174503)
Try building the index for "genome.fa" first:

Code:

bowtie2-build genome.fa genome
Then "-x genome" would be the proper method to specify where the indices are (from your current path at least).

Thanks for the reply. I tried that and got a Error. Empty fasta? This is a index I downloaded from I genome

http://i.imgur.com/ikTric7.png

dpryan 06-09-2015 12:26 AM

Presumably the fasta file is empty or non-existent then.

Milestailsprowe 06-09-2015 12:27 AM

Quote:

Originally Posted by dpryan (Post 174507)
Presumably the fasta file is empty or non-existent then.

The genome.fa file? and if so how should I go about fixing that because its from the Igenome Cow set

dpryan 06-09-2015 12:38 AM

Well, have a look at the file. How big is it? Does it actually exist? If it does exist and seems to have a reasonable size, is it where you're telling bowtie2?

Milestailsprowe 06-09-2015 01:49 AM

Quote:

Originally Posted by dpryan (Post 174509)
Well, have a look at the file. How big is it? Does it actually exist? If it does exist and seems to have a reasonable size, is it where you're telling bowtie2?

Honestly it exist and all that. Checked it out in linux and windows.

http://i.imgur.com/6kHSvFv.jpg

dpryan 06-09-2015 01:52 AM

Given the file names, you want "-x genome", not "-x genome.fa". The documentation on this could probably be improved.

BTW, it looks like the fasta file has serious problems. It should be MUCH larger than 1KB.

GenoMax 06-09-2015 02:16 AM

@Milestailsprowe: That genome.fa may be a softlink for the full genome.fa file in the "WholeGenomeFasta" directory under the "Sequence" folder. Can you check to see if that file is large?

Do yourself a favor and don't use spaces in names (external drives/files/directories). It is going to get you in trouble down the road. Anytime you feel like using a space replace that with an "_".

Milestailsprowe 06-09-2015 02:45 PM

Quote:

Originally Posted by GenoMax (Post 174523)
@Milestailsprowe: That genome.fa may be a softlink for the full genome.fa file in the "WholeGenomeFasta" directory under the "Sequence" folder. Can you check to see if that file is large?

Do yourself a favor and don't use spaces in names (external drives/files/directories). It is going to get you in trouble down the road. Anytime you feel like using a space replace that with an "_".

Doesnt look to be any different sadly
http://i.imgur.com/Ce0hsOQ.jpg

GenoMax 06-09-2015 06:37 PM

It appears that in one our your attempts to run bowtie you may have overwritten the original genome.fa file (you can see that genome.fa has a current "modified" date where as the rest of the files are dated from 2012/2013) .

If you have the original tar archive you should re-extract it to restore the original set of files/folders. If not, you will need to re-download the tar archive from iGenomes.

Milestailsprowe 06-09-2015 10:11 PM

Quote:

Originally Posted by GenoMax (Post 174630)
It appears that in one our your attempts to run bowtie you may have overwritten the original genome.fa file (you can see that genome.fa has a current "modified" date where as the rest of the files are dated from 2012/2013) .

If you have the original tar archive you should re-extract it to restore the original set of files/folders. If not, you will need to re-download the tar archive from iGenomes.

Ok untared another one and now have a 2.7gig File thanks. Should I try to align the file in the WHOLE gene folder or the one in the bowtie2 index

GenoMax 06-10-2015 02:02 AM

You should align using bowtie2 index (you only specify "basename" of the index). Option to use in your case (replace full_path_to with real value) will be

Code:

-x /full_path_to/Sequence/Bowtie2Index/genome

Milestailsprowe 06-10-2015 07:06 PM

Quote:

Originally Posted by GenoMax (Post 174668)
You should align using bowtie2 index (you only specify "basename" of the index). Option to use in your case (replace full_path_to with real value) will be

Code:

-x /full_path_to/Sequence/Bowtie2Index/genome

Fixed the wrong command

emma2019 10-17-2019 04:34 PM

exit with code 1
 
Quote:

Originally Posted by Milestailsprowe (Post 174742)
Fixed the wrong command

Hi, how do you solve your problems by re-downloaded the genome from iGenomes? Do you regenerate the indexes based on the new genome from iGenomes?
I am also running to the same issue.


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