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LANL-Bioinformatics / EDGE

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
https://lanl-bioinformatics.github.io/EDGE/
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Edge #52

Closed smlary closed 1 year ago

smlary commented 3 years ago

Describe the bug I am running an 18S amplicon analysis on QIIME2 and when I run it a taxonomy plot is not produced. I have ran it many times and the result does not change. I ran it on 16s/18S silva and used Dada2 with truncation of F(280) and R(240). sampling depth was 1000 and was set to adjust if needed. Screen Shot 2020-11-14 at 1 54 48 PM Screen Shot 2020-11-14 at 1 55 06 PM

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chienchi commented 3 years ago

Hi,

Thanks for post the issue and have screenshot attached. These help us identifying the issue much easier and solve it. The main issue here is the space in the sampleID of the Metadata Mapping File from user input, like sample 10. One of the qiime2 tool (vsearch dereplicate-sequences) doesn't accept spaces in the sampleID. We have update the code to replace the space to "-" for user (sample 10 to sample-10) and deployed on edgebioinforamtics.org site. Please empty the project and rerun it to see if the issue fixed.

The other issue #53 may be also caused by the same reason. Please also try to empty and rerun the project.

Thanks, Chienchi

smlary commented 3 years ago

Thanks Chienchi, I re-ran it and I am having the same problem. Sincerely, Sean Lary

On Mon, Nov 16, 2020 at 1:45 PM Chien-Chi Lo notifications@github.com wrote:

Hi,

Thanks for post the issue and have screenshot attached. These help us identifying the issue much easier and solve it. The main issue here is the space in the sampleID of the Metadata Mapping File from user input, like sample

  1. One of the qiime2 tool (vsearch dereplicate-sequences) doesn't accept spaces in the sampleID. We have update the code to replace the space to "-" for user (sample 10 to sample-10) and deployed on edgebioinforamtics.org site. Please empty the project and rerun it to see if the issue fixed.

The other issue #53 https://github.com/LANL-Bioinformatics/EDGE/issues/53 may be also caused by the same reason. Please also try to empty and rerun the project.

Thanks, Chienchi

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/LANL-Bioinformatics/EDGE/issues/52#issuecomment-728428277, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARYGQRYRDZZIHYJEIPMV44DSQG2RZANCNFSM4TV2XDTA .

-- Sean M. Lary, MS University of Hawai'i Microbiology Department 1960 East-West Road Biomedical 603 Honolulu, HI 96822

chienchi commented 3 years ago

Thanks for rerun it and we found there are two more issue here. One is the space in the metadata header field and category value. In your data, the example is "Sample Type". We have fixed it by automatically correct it and replace it with "-". The second issue that the taxonomy classifier is memory intensive step. The public edge instance may run out of memory if there are other projects running at the same time. I have the taxonomy done on your project (18S-AVW_Seamount_edited_fixed) when there is no other projects running. In the future, please rerun it if it is happened.

smlary commented 3 years ago

Chien-Chi Lo, Thank you! I have a project labeled 16S_AVW_Seamount and It does not have any Beta-diversity information. Could this also be due to a faulty mapping file? Here is the information regarding this project. Project Summary Description: UPDATED SEAMOUNT Submission Time: 2020 Nov 10 20:38:51 (UTC) Number of CPUs: 14 Project Status: Complete Total Analysis Run Time: 01:27:55 Last Run Time: 01:27:55 Owner: slary@hawaii.edu

On Wed, Nov 18, 2020 at 1:54 PM Chien-Chi Lo notifications@github.com wrote:

Thanks for rerun it and we found there are two more issue here. One is the space in the metadata header field and category value. In your data, the example is "Sample Type". We have fixed it by automatically correct it and replace it with "-". The second issue that the taxonomy classifier is memory intensive step. The public edge instance may run out of memory if there are other projects running at the same time. I have the taxonomy done on your project (18S-AVW_Seamount_edited_fixed) when there is no other projects running. In the future, please rerun it if it is happened.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/LANL-Bioinformatics/EDGE/issues/52#issuecomment-730031074, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARYGQR43CHYADMPARW4ZKB3SQRNDNANCNFSM4TV2XDTA .

-- Sean M. Lary, MS University of Hawai'i Microbiology Department 1960 East-West Road Biomedical 603 Honolulu, HI 96822

chienchi commented 3 years ago

Yes. After the metadata mapping file fixed, the reran has show the beta-diversity info.