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Jon Colman
Jan 15
mNGS vs 16s
I have a question regarding what pipelines to use. Can I run 16s sequences through the Run Edge or
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mNGS vs 16s
I have a question regarding what pipelines to use. Can I run 16s sequences through the Run Edge or
Jan 15
Amy Xiao
,
Lo, Chien-Chi
4
12/11/23
Questions on local installation of EDGE
Hi Amy, No problem at all. For the 4.1.5, you do need Mysql installed and someone with mysql root
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Questions on local installation of EDGE
Hi Amy, No problem at all. For the 4.1.5, you do need Mysql installed and someone with mysql root
12/11/23
wudtichai manasatienkij
9/1/23
Registration
Hi, Could you please help me, check the registration of my colleague (pthip...@gmail.com,
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Registration
Hi, Could you please help me, check the registration of my colleague (pthip...@gmail.com,
9/1/23
wudtichai manasatienkij
8/17/23
Align Trim: Failure
Hi, I performed mapping with align trim but it failed because no read remain after align trim. I
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Align Trim: Failure
Hi, I performed mapping with align trim but it failed because no read remain after align trim. I
8/17/23
Josie Blair
,
Lo, Chien-Chi
4
1/18/23
ShortBred AMR data
Thanks so much you've been so helpful! Sent from my iPhone On Jan 18, 2023, at 3:36 PM, Lo, Chien
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ShortBred AMR data
Thanks so much you've been so helpful! Sent from my iPhone On Jan 18, 2023, at 3:36 PM, Lo, Chien
1/18/23
wudtichai manasatienkij
,
Lo, Chien-Chi
2
1/3/23
ERROR install both EDGE Bioinformatics and EDGE-COVID19 docker
Hi, We have running EDGE and EDGE-COVID19 guide on docker hub. EDGE-COVID19 https://hub.docker.com/r/
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ERROR install both EDGE Bioinformatics and EDGE-COVID19 docker
Hi, We have running EDGE and EDGE-COVID19 guide on docker hub. EDGE-COVID19 https://hub.docker.com/r/
1/3/23
Lo, Chien-Chi
9/9/22
Re: [EXTERNAL] Troubleshooting Failed Analysis
Hi Pratibha, Thanks for using EDGE. We have checked the project you ran and found the input, Qiime2
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Re: [EXTERNAL] Troubleshooting Failed Analysis
Hi Pratibha, Thanks for using EDGE. We have checked the project you ran and found the input, Qiime2
9/9/22
Matthieu Simonin
6/16/22
Zun down ?
Hi, I've got some trouble with Zun lately at Chi-Edge. The symptoms include: - dangling
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Zun down ?
Hi, I've got some trouble with Zun lately at Chi-Edge. The symptoms include: - dangling
6/16/22
Luz Vargas
,
Lo, Chien-Chi
2
8/4/21
EDGE: Run Time
Thanks for using EDGE. With constraint resource, EDGE limits three projects to run at same time.
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EDGE: Run Time
Thanks for using EDGE. With constraint resource, EDGE limits three projects to run at same time.
8/4/21
t k
, …
Lo, Chien-Chi
6
2/3/21
limited number of genomes
Sorry! Editing the configuration will allow more genomes been processed by the back-end command lines
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limited number of genomes
Sorry! Editing the configuration will allow more genomes been processed by the back-end command lines
2/3/21
Lo, Chien-Chi
12/3/20
EDGE 2.4.0 release
Dear EDGE users, We have EDGE v2.4.0 version released. Below are some highlight new features and you
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EDGE 2.4.0 release
Dear EDGE users, We have EDGE v2.4.0 version released. Below are some highlight new features and you
12/3/20
Dinesh Kumar
,
Lo, Chien-Chi
2
3/4/19
ERROR: Permission denied. Only project owner can perform this action.
Hi, Most of projects actions are only for project owners. Do you mean you own the project but still
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ERROR: Permission denied. Only project owner can perform this action.
Hi, Most of projects actions are only for project owners. Do you mean you own the project but still
3/4/19
gmoore777
,
Lo, Chien-Chi
2
1/28/19
Projects: Private --> Public --> Private
The toggle to make a project to private is only available on the single project mode. User can see
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Projects: Private --> Public --> Private
The toggle to make a project to private is only available on the single project mode. User can see
1/28/19
gmoore777
,
Lo, Chien-Chi
3
1/18/19
Docker: Logging in: Could not connect to address=(host=localhost)(port=3306)(type=master)
It's glad to hear you have all set now. The docker page has been updated; Thanks. From: <edge-
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Docker: Logging in: Could not connect to address=(host=localhost)(port=3306)(type=master)
It's glad to hear you have all set now. The docker page has been updated; Thanks. From: <edge-
1/18/19
gmoore777
,
Lo, Chien-Chi
3
1/17/19
[bwt_restore_sa] Failed to allocate 16473698552 bytes
Thank you for your reply. Since my problem, I kept the large BWA index files, but I up-sized my Linux
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[bwt_restore_sa] Failed to allocate 16473698552 bytes
Thank you for your reply. Since my problem, I kept the large BWA index files, but I up-sized my Linux
1/17/19
gmoore777
3
1/16/19
Docker Installation: What ar the username/password for the 2 URLs and the Container/Docker_machine?
The short story, is I'm all set for now. ---------------------- The long story is: 1.) The
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Docker Installation: What ar the username/password for the 2 URLs and the Container/Docker_machine?
The short story, is I'm all set for now. ---------------------- The long story is: 1.) The
1/16/19
Леонид Солнцев
,
Lo, Chien-Chi
4
12/17/18
Error uploading files (Ubuntu 18.04, EDGE as docker)
No. It is on the github only. Will do the docker update later. If you cannot wait the docker image
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Error uploading files (Ubuntu 18.04, EDGE as docker)
No. It is on the github only. Will do the docker update later. If you cannot wait the docker image
12/17/18
gmoore777
, …
Lo, Chien-Chi
9
11/28/18
Edge: running the Qiime analysis: what is the metadata mapping file?
1.)That worked: "De-multiplexed Reads Dir" with a metadata mapping file of listing only
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Edge: running the Qiime analysis: what is the metadata mapping file?
1.)That worked: "De-multiplexed Reads Dir" with a metadata mapping file of listing only
11/28/18
Anderson, Joseph J (Joe) CIV USARMY 21 SIG BDE (USA)
11/28/18
RE: [Non-DoD Source] Re: Edge: running the Qiime analysis: what is the metadata mapping file? (UNCLASSIFIED)
CLASSIFICATION: UNCLASSIFIED Hi All, I just wanted to chime in, that's a pretty good project name
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RE: [Non-DoD Source] Re: Edge: running the Qiime analysis: what is the metadata mapping file? (UNCLASSIFIED)
CLASSIFICATION: UNCLASSIFIED Hi All, I just wanted to chime in, that's a pretty good project name
11/28/18
gmoore777
,
Lo, Chien-Chi
6
11/27/18
gottcha.py: error: Incorrect BWA index: missing ... RefSeq-Release89.Virus.species.fna.gz.amb
Sorry for confusion on all this again. EDGE is under active development. Unless users are familiar
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gottcha.py: error: Incorrect BWA index: missing ... RefSeq-Release89.Virus.species.fna.gz.amb
Sorry for confusion on all this again. EDGE is under active development. Unless users are familiar
11/27/18
Elinor Pulcini
,
Lo, Chien-Chi
2
11/27/18
Phred error
If you can check or provide some log files in the QiimeAnalysis directory, and those should have more
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Phred error
If you can check or provide some log files in the QiimeAnalysis directory, and those should have more
11/27/18
gmoore777
,
Lo, Chien-Chi
5
11/21/18
Error on all the "gotcha-" Classifications
Thanks. I found the gottcha package come with compiled perl modules which doesn't work on the
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Error on all the "gotcha-" Classifications
Thanks. I found the gottcha package come with compiled perl modules which doesn't work on the
11/21/18
gmoore777
11/16/18
Edge on Ubuntu 18.04: convert-im6.q16: not authorized `.../QC_qc_report.pdf'
To myself: --------- Problem: In error.log, I saw many of these errors: convert-im6.q16: not
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Edge on Ubuntu 18.04: convert-im6.q16: not authorized `.../QC_qc_report.pdf'
To myself: --------- Problem: In error.log, I saw many of these errors: convert-im6.q16: not
11/16/18
gmoore777
,
Lo, Chien-Chi
3
11/16/18
Edge on Ubuntu 18.04: UserManagement: Manage Projects: ORDER BY clause is not in SELECT list
Chienchi Thank you, that solved the problem. Guy Note to self: I actually added those 2 lines, under
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Edge on Ubuntu 18.04: UserManagement: Manage Projects: ORDER BY clause is not in SELECT list
Chienchi Thank you, that solved the problem. Guy Note to self: I actually added those 2 lines, under
11/16/18
Lo, Chien-Chi
,
Леонид Солнцев
3
10/31/18
Re: Edge installation on Ubuntu - error when trying to set up an admin user
I've ovrecomed it by removing NOT NULL constrain and then copying value of password field into
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Re: Edge installation on Ubuntu - error when trying to set up an admin user
I've ovrecomed it by removing NOT NULL constrain and then copying value of password field into
10/31/18
Scott
,
Lo, Chien-Chi
3
10/16/18
Extract mapped sequences classified with GOTTCHA viral database
Thank you. On Monday, October 15, 2018 at 4:05:56 PM UTC-6, Lo, Chien-Chi wrote: Hi Scott, This is
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Extract mapped sequences classified with GOTTCHA viral database
Thank you. On Monday, October 15, 2018 at 4:05:56 PM UTC-6, Lo, Chien-Chi wrote: Hi Scott, This is
10/16/18
Scott
,
Lo, Chien-Chi
4
10/11/18
cannot access reports from using the EDGE_gui
Resolved this issue by opening up permissions to the folder ( chmod 0777) as suggested on the bioedge
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cannot access reports from using the EDGE_gui
Resolved this issue by opening up permissions to the folder ( chmod 0777) as suggested on the bioedge
10/11/18
Scott
, …
Chain, Patrick Sam Guy
5
9/20/18
assembly times using lrasm
I ran the assembly today without error correction. Assembly time dropped from 60hrs to 1hr 44min.
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assembly times using lrasm
I ran the assembly today without error correction. Assembly time dropped from 60hrs to 1hr 44min.
9/20/18
Scott
,
Lo, Chien-Chi
3
9/13/18
Nanopore assembly and PanGIA
Thanks for the quick reply. PanGIA pipeline is working with nanopore reads. Scott
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Nanopore assembly and PanGIA
Thanks for the quick reply. PanGIA pipeline is working with nanopore reads. Scott
9/13/18
Леонид Солнцев
,
Lo, Chien-Chi
3
11/12/17
Broken db archive
thanks for answer. i'l try to redownload it. понедельник, 13 ноября 2017 г., 6:59:11 UTC+3
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Broken db archive
thanks for answer. i'l try to redownload it. понедельник, 13 ноября 2017 г., 6:59:11 UTC+3
11/12/17