merge-detail for fungal its

[dbrami]

Hi I'm getting the following error:

cmd-> java -Xmx16g -jar /bio_bin/rdp_classifier_2.10.1/dist/classifier.jar merge-detail \
> -o combined_rdp.txt -h combined_hierarchy.txt -c 0.5 --gene fungalits_unite \
> S14MNOARP5.trimmed.noplant/S14MNOARP5.trimmed.noplant_UNITE_public_30.12.2014_UniVec.ovl.dusted.valid.rdp.tmp \
> S14MNOAEP5.trimmed.noplant/S14MNOAEP5.trimmed.noplant_UNITE_public_30.12.2014_UniVec.ovl.dusted.valid.rdp.tmp
Command Error: fungalits_unite is NOT valid, only allows 16srrna, fungallsu, fungalits_warcup and fungalits_unite

Any ideas why? The classification portion worked without issue.

[rdpstaffmsu]

Dear Daniel,

Would you send the two input files to us to test? Thank you.

Sincerely,

Benli Chai RDP Staff

On Fri, Feb 27, 2015 at 2:15 PM, Daniel Brami notifications@github.com wrote:

Hi I'm getting the following error:

cmd-> java -Xmx16g -jar /bio_bin/rdp_classifier_2.10.1/dist/classifier.jar merge-detail > -o combined_rdp.txt -h combined_hierarchy.txt -c 0.5 --gene fungalits_unite > S14MNOARP5.trimmed.noplant/S14MNOARP5.trimmed.noplant_UNITE_public_30.12.2014_UniVec.ovl.dusted.valid.rdp.tmp > S14MNOAEP5.trimmed.noplant/S14MNOAEP5.trimmed.noplant_UNITE_public_30.12.2014_UniVec.ovl.dusted.valid.rdp.tmp Command Error: fungalits_unite is NOT valid, only allows 16srrna, fungallsu, fungalits_warcup and fungalits_unite

Any ideas why?

— Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/7.

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[dbrami]

Hello Benli, Forgive me but I can't figure out how to attach files to an issue if the files are not of the graphical type. Please suggest the best method.

[dbrami]

Hi Benli, Is there an email address I can send the files to?

[rdpstaffmsu]

Hi, Daniel,

Please send to rdpstaff@msu.edu. Thank you.

Benli

On Mon, Mar 2, 2015 at 1:26 PM, Daniel Brami notifications@github.com wrote:

Hi Benli, Is there an email address I can send the files to?

— Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/7#issuecomment-76770335.

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[dbrami]

Thank you for the email response. I have cloned a copy of the classifier repo but the 'dist' and 'lib' folders are not part of this cloned repo. I do not want to venture into assuming how to compile this properly. Any suggestions so that I may test again?

[rdpstaffmsu]

Hi, Daniel,

The best is to clone the entire RDPTools package ( https://github.com/rdpstaff/RDPTools) since the classifier has dependencies on a couple other utilities. The procedure is:

After cloning this repository enter the commands:

Initial Project Set Up

$ git submodule init $ git submodule update

then type 'make'

Let me know there is a problem.

Benli

On Mon, Mar 2, 2015 at 5:19 PM, Daniel Brami notifications@github.com wrote:

Thank you for the email response. I have cloned a copy of the classifier repo but the 'dist' and 'lib' folders are not part of this cloned repo. I do not want to venture into assuming how to compile this properly. Any suggestions so that I may test again?

— Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/7#issuecomment-76839009.

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[dbrami]

Worked like a charm - thanks for the help!