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Old 06-08-2015, 10:49 PM   #1
Milestailsprowe
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Default 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?

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Old 06-08-2015, 11:08 PM   #2
dpryan
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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).
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Old 06-08-2015, 11:19 PM   #3
Milestailsprowe
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Quote:
Originally Posted by dpryan View Post
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

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Old 06-08-2015, 11:26 PM   #4
dpryan
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Presumably the fasta file is empty or non-existent then.
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Old 06-08-2015, 11:27 PM   #5
Milestailsprowe
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Quote:
Originally Posted by dpryan View Post
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
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Old 06-08-2015, 11:38 PM   #6
dpryan
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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?
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Old 06-09-2015, 12:49 AM   #7
Milestailsprowe
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Quote:
Originally Posted by dpryan View Post
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.

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Old 06-09-2015, 12:52 AM   #8
dpryan
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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.
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Old 06-09-2015, 01:16 AM   #9
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@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 "_".
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Old 06-09-2015, 01:45 PM   #10
Milestailsprowe
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Quote:
Originally Posted by GenoMax View Post
@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
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Old 06-09-2015, 05:37 PM   #11
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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.

Last edited by GenoMax; 06-09-2015 at 05:41 PM.
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Old 06-09-2015, 09:11 PM   #12
Milestailsprowe
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Quote:
Originally Posted by GenoMax View Post
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
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Old 06-10-2015, 01:02 AM   #13
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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
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Old 06-10-2015, 06:06 PM   #14
Milestailsprowe
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Quote:
Originally Posted by GenoMax View Post
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

Last edited by Milestailsprowe; 06-10-2015 at 06:53 PM.
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