Groups

shortbred-users

Contact owners and managers

1–30 of 66

Hello ShortBRED users!

Please direct all future questions about ShortBRED to our new Discourse forum: https://forum.biobakery.org/.
This forum can be viewed by anyone, but you will need to ***create an account to post a new question***.

This Google Group is now set as "read only": You may continue to browse existing message threads within the Group, but new messages sent to the Group will bounce back as "undeliverable."

0 selected

Daniel Barich, … Joan Slonczewski7

12/3/22

error running shortbred-identify

Besides CARD (for drug resistance) what other databases do you find produce good markers for

unread,

error running shortbred-identify

Besides CARD (for drug resistance) what other databases do you find produce good markers for

12/3/22

12/16/19

shortbred_quantify.py error: cannot concatenate 'str' and 'list' objects [line 558 of quantify_functions.py]

I am running into the following error when trying to run shortbred_quantify.py: Tabulating results

unread,

shortbred_quantify.py error: cannot concatenate 'str' and 'list' objects [line 558 of quantify_functions.py]

I am running into the following error when trying to run shortbred_quantify.py: Tabulating results

12/16/19

Joan Slonczewski, Eric Franzosa4

12/13/19

Optimal reads to get for ShortBRED

Eric, is there any chance you could help out Daniel Barich on his question about the ShortBRED run

unread,

Optimal reads to get for ShortBRED

Eric, is there any chance you could help out Daniel Barich on his question about the ShortBRED run

12/13/19

Daniel Barich, … Joan Slonczewski3

11/19/19

problem running shortbred-quantify

Eric, Thanks so much for helping out! I have a lab of 15 undergrads starting to run resistomes on

unread,

problem running shortbred-quantify

Eric, Thanks so much for helping out! I have a lab of 15 undergrads starting to run resistomes on

11/19/19

Daniel Barich, Eric Franzosa3

11/18/19

Re: ShortBRED help installing

Agreed Daniel and thanks for bringing this to our attention. Thanks, Eric On Tue, Nov 12, 2019 at 9:

unread,

Re: ShortBRED help installing

Agreed Daniel and thanks for bringing this to our attention. Thanks, Eric On Tue, Nov 12, 2019 at 9:

11/18/19

Levesque, Nicole M.

11/14/19

From: Joan Slonczewski <slonc...@kenyon.edu> Sent: Monday, November 11, 2019 4:12 PM To:

unread,

From: Joan Slonczewski <slonc...@kenyon.edu> Sent: Monday, November 11, 2019 4:12 PM To:

11/14/19

Camila Castillo

11/8/19

Resistance class according to CARD markers in Shortbred biobakery

Hi, For running my shortbred analysis, I used the CARD 2017 markers in the Shortbred biobakery

unread,

Resistance class according to CARD markers in Shortbred biobakery

Hi, For running my shortbred analysis, I used the CARD 2017 markers in the Shortbred biobakery

11/8/19

Violetta Florova

8/8/19

Can we correlate the number of counts with transcriptional activity in bacterial genome?

Dear ShortBred developers and users, How can we interpret the higher number of counts across

unread,

Can we correlate the number of counts with transcriptional activity in bacterial genome?

Dear ShortBred developers and users, How can we interpret the higher number of counts across

8/8/19

Violetta Florova

8/8/19

Consistent zero counts and multiple hits for the marker

Dear All, I have received consistent zero counts and variable hits for one of my markers while

unread,

Consistent zero counts and multiple hits for the marker

Dear All, I have received consistent zero counts and variable hits for one of my markers while

8/8/19

Violetta Florova, Eric Franzosa4

7/3/19

Shortbred Identify BLAST database error

I'm really sorry, I can't find why the code keeps crashing. It work good when I use "

unread,

Shortbred Identify BLAST database error

I'm really sorry, I can't find why the code keeps crashing. It work good when I use "

7/3/19

Violetta Florova

4/9/19

Shortbred vs HumanN in order to analyse nitrogen bacteria metabolism

Dear ALL, I was wondering what is the main difference between ShortBRED and HumanN? I have built the

unread,

Shortbred vs HumanN in order to analyse nitrogen bacteria metabolism

Dear ALL, I was wondering what is the main difference between ShortBRED and HumanN? I have built the

4/9/19

shriram patel, Eric Franzosa2

2/6/19

Families with multiple markers

Hi Shriram, The algorithm focuses on the median coverage of each family's markers. Hence, if

unread,

Families with multiple markers

Hi Shriram, The algorithm focuses on the median coverage of each family's markers. Hence, if

2/6/19

Curtis Huttenhower, Modupe Coker2

12/5/18

Re: query about shortbred

I look forward to the response to this question as well. I also used usearch11.0.667_i86linux32. On

unread,

Re: query about shortbred

I look forward to the response to this question as well. I also used usearch11.0.667_i86linux32. On

12/5/18

Violetta Florova, Dave Yarmosh2

12/5/18

Error with creating markers using uniref 100: Command '['makeblastdb returned non-zero exit status 1

Hi Violetta, Have you tried using the makeblastdb command from your command line, instead of doing it

unread,

Error with creating markers using uniref 100: Command '['makeblastdb returned non-zero exit status 1

Hi Violetta, Have you tried using the makeblastdb command from your command line, instead of doing it

12/5/18

12/5/18

Alternative to Muscle

Hi everyone, ShortBRED is great and I'm including it in a common workflow of mine. I'm

unread,

Alternative to Muscle

Hi everyone, ShortBRED is great and I'm including it in a common workflow of mine. I'm

12/5/18

11/5/18

metadata associated with updated Virulence Factor markers

Hi, ShortBred team, I downloaded the updated VF markers, but noticed there is no metadata associated

unread,

metadata associated with updated Virulence Factor markers

Hi, ShortBred team, I downloaded the updated VF markers, but noticed there is no metadata associated

11/5/18

Violetta Florova

9/24/18

seqdbio.cpp(221) assert failed: BufferCount > 0 - interesting error!

Hello! I've got quite interesting error in 4 markers library out of 53. I run this K00370 markers

unread,

seqdbio.cpp(221) assert failed: BufferCount > 0 - interesting error!

Hello! I've got quite interesting error in 4 markers library out of 53. I run this K00370 markers

9/24/18

davejac...@gmail.com

9/19/18

Issue with test dataset

Hello, I'm having an issue with generating the expected results from the data provided in the “

unread,

Issue with test dataset

Hello, I'm having an issue with generating the expected results from the data provided in the “

9/19/18

Levesque, Nicole M., Eric Franzosa2

8/13/18

FW: Help with ShortBRED : Sam Davison

Hi Samuel, Sorry for the delayed reply - is it possible to include the specific error messages that

unread,

FW: Help with ShortBRED : Sam Davison

Hi Samuel, Sorry for the delayed reply - is it possible to include the specific error messages that

8/13/18

gils...@gmail.com

6/18/18

Minimum sequencing depth for ShortBRED (human fecal sample)

Hello All, We are planning a sequencing experiment with human gut microbiomes in search for specific

unread,

Minimum sequencing depth for ShortBRED (human fecal sample)

Hello All, We are planning a sequencing experiment with human gut microbiomes in search for specific

6/18/18

Nsa Dada, … Dave Yarmosh19

4/9/18

Help with generating markers.

Hi Jim, Any updates to this? I've just encountered the same issue with this -- Traceback (most

unread,

Help with generating markers.

Hi Jim, Any updates to this? I've just encountered the same issue with this -- Traceback (most

4/9/18

kuangd...@gmail.com, … Violetta Florova5

2/26/18

Quantify antibiotic resistance protein families on bacterial isolate genomes

Dear Jim, Thank you for your explanation again. I run agains ShortBRED_ARDB_Evaluation_markers - it

unread,

Quantify antibiotic resistance protein families on bacterial isolate genomes

Dear Jim, Thank you for your explanation again. I run agains ShortBRED_ARDB_Evaluation_markers - it

2/26/18

Violetta Florova, Jim Kaminski2

2/24/18

Does Shortbred.quantify generate empty results. file?

Hi Violetta, I think this might be due to the extension on the filenames. If these are labeled as

unread,

Does Shortbred.quantify generate empty results. file?

Hi Violetta, I think this might be due to the extension on the filenames. If these are labeled as

2/24/18

Jim Kaminski, Violetta Florova3

2/24/18

Re: TypeError: cannot concatenate 'str' and 'list' objects

Hi Violetta, Thank you for your patience. It looks like the issue is that the wgs file has a fastq

unread,

Re: TypeError: cannot concatenate 'str' and 'list' objects

Hi Violetta, Thank you for your patience. It looks like the issue is that the wgs file has a fastq

2/24/18

Dave Yarmosh, Eric Franzosa3

1/11/18

Identifying marker locations on a reference genome

Hi Dave, If you want to know the precise location of the marker inside a genome (especially a new

unread,

Identifying marker locations on a reference genome

Hi Dave, If you want to know the precise location of the marker inside a genome (especially a new

1/11/18

Violetta Florova

12/14/17

ErrNo 32 during building markers database

How can I solve this error? *** ERROR *** Cannot open 'tmp115201513281346060/clust/fams/tr|

unread,

ErrNo 32 during building markers database

How can I solve this error? *** ERROR *** Cannot open 'tmp115201513281346060/clust/fams/tr|

12/14/17

YJ Kim, Jim Kaminski2

12/10/17

CD-HIT identity %

Hi Younjung, You can obtain 100% id with cd-hit by using these parameter settings: --clustid 1.0 --

unread,

CD-HIT identity %

Hi Younjung, You can obtain 100% id with cd-hit by using these parameter settings: --clustid 1.0 --

12/10/17

YJ Kim, Jim Kaminski2

11/13/17

invalid command line Option --makeudb_usearch is invalid

Hi Younjung, Which version of usearch are you using? Thanks, Jim On Mon, Nov 13, 2017 at 4:22 AM, YJ

unread,

invalid command line Option --makeudb_usearch is invalid

Hi Younjung, Which version of usearch are you using? Thanks, Jim On Mon, Nov 13, 2017 at 4:22 AM, YJ

11/13/17

Giorgio Casaburi, … Eric Franzosa5

10/30/17

Merging outputs from multiple samples

Hi Eric, 1000 thanks for the clarification. It's great to know the difference between the two

unread,

Merging outputs from multiple samples

Hi Eric, 1000 thanks for the clarification. It's great to know the difference between the two

10/30/17

Eric Franzosa, Aram Avila-Herrera3

8/31/17

Re: CARD version and marker to sequence/ARO mapping

Hi Aram, I haven't looked closely at the individual clusters myself. ShortBRED's default is

unread,

Re: CARD version and marker to sequence/ARO mapping

Hi Aram, I haven't looked closely at the individual clusters myself. ShortBRED's default is

8/31/17

Search

Clear search

Close search

Google apps

Main menu