Open s1081289 opened 8 years ago
wwood
commented
8 years ago Hi there. It looks as if there might be something amiss with an input .bam file, because of this line:
[W::sam_hdr_read] bgzf_check_EOF: Value too large for defined data typeThis line comes from the samtools code itself (well, libhts). I imagine you should be able to recreate outside of groopm by doing something like this
samtools view your.bam >/dev/nullSo I would suggest redoing your mapping. Hope that helps.
s1081289
commented
8 years ago Thank you for your fast respons. Samtools view didn't print anything out to stderr as you can see in the picture:
After I did that I have also tried to run groopM again with an different order of bammfiles, with no succes.
Van: Ben J Woodcroft notifications@github.com Verzonden: donderdag 3 december 2015 12:14 Aan: Ecogenomics/GroopM CC: Nispeling, Danny Onderwerp: Re: [GroopM] Error with parsing groopM (#18)
Hi there. It looks as if there might be something amiss with an input .bam file, because of this line:
[W::sam_hdr_read] bgzf_check_EOF: Value too large for defined data type
This line comes from the samtools code itself (well, libhts). I imagine you should be able to recreate outside of groopm by doing something like this
samtools view your.bam >/dev/null
So I would suggest redoing your mapping. Hope that helps.
Reply to this email directly or view it on GitHubhttps://github.com/Ecogenomics/GroopM/issues/18#issuecomment-161601779.
Error with parsing groopM · Issue #18 · Ecogenomics/GroopMhttps://github.com/Ecogenomics/GroopM/issues/18#issuecomment-161601779 github.com Hello, I've a problem with groopM. When I tried to create the database with the command: groopm parse db.gm contigs.fa *.bam I get the following error: We have made the BAMM-files with samtools...
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wwood
commented
8 years ago Strange, any chance you could redo your mapping to check? How are you mapping anyway?
s1081289
commented
8 years ago The mapping and generating of the bamfiles was done using the preprocessing steps from another binning tool, named "CONCOCT".
The methods that are used to do te mapping are
You can see the code in this script:
https://docs.google.com/document/d/1jowt-reSN4B1Is_KRM5ao34qX_JqJUpfMxXYHTPATFU
The sorting after the mapping we have done with this code (samtools):
https://drive.google.com/file/d/0B9PKyUBXcC-GTE1IVy1BODVRdVU/view?usp=sharing
I don't think I can do the mapping again, becuase I didn't get hours for doing te mapping, from my supervisor.
Van: Ben J Woodcroft notifications@github.com Verzonden: zondag 6 december 2015 4:46 Aan: Ecogenomics/GroopM CC: Nispeling, Danny Onderwerp: Re: [GroopM] Error with parsing groopM (#18)
Strange, any chance you could redo your mapping to check? How are you mapping anyway?
Reply to this email directly or view it on GitHubhttps://github.com/Ecogenomics/GroopM/issues/18#issuecomment-162268618.
Error with parsing groopM · Issue #18 · Ecogenomics/GroopMhttps://github.com/Ecogenomics/GroopM/issues/18#issuecomment-162268618 github.com Hello, I've a problem with groopM. When I tried to create the database with the command: groopm parse db.gm contigs.fa *.bam I get the following error: We have made the BAMM-files with samtools...
Op deze e-mail zijn de voorwaarden van toepassing als vermeld op: The following conditions apply to this e-mail: http://www.hsleiden.nl/disclaimer-email
Hello,
I've a problem with groopM. When I tried to create the database with the command: groopm parse db.gm contigs.fa *.bam I get the following error:
We have made the BAMM-files with samtools.
I know I have Installed groopM right because I have tried it before with another dataset and it worked as expected.
thanks in advance