EMIRGE users

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This forum serves to support the EMIRGE software. EMIRGE reconstructs rRNA genes from short-read sequencing data.

Note that this forum is moderated to reduce spam. If your message doesn't appear immediately, please be patient until it is approved for posting.

Publications (please cite if appropriate):

Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF: EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome biology 2011, 12:R44. [Open Access Article]

Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF: Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments. PLoS ONE 2013, 8:e56018. [Open Access Article]

Code:

https://github.com/csmiller/EMIRGE

Wiki, including Frequently Asked Questions (FAQ):

https://github.com/csmiller/EMIRGE/wiki

0 selected

2/10/22

IndexError: list index out of range

Dear Emirge support Kindly assist in how best this can be solved I ran emirge through the following

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IndexError: list index out of range

Dear Emirge support Kindly assist in how best this can be solved I ran emirge through the following

2/10/22

mariarovis...@gmail.com, もみもみお2

10/23/20

I think that you should do like this -b /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/

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I think that you should do like this -b /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/

10/23/20

xvaz...@gmail.com, … hem...@uoguelph.ca6

3/5/20

Hi Chris, I'm getting the exact same error than Bryan, 3 years later. Any news on that error?

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Hi Chris, I'm getting the exact same error than Bryan, 3 years later. Any news on that error?

3/5/20

alana....@gmail.com

2/27/19

Installing EMIRGE using conda

Has anyone successfully done this? I am able to install EMIRGE but when I try to run emirge.py, I get

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Installing EMIRGE using conda

Has anyone successfully done this? I am able to install EMIRGE but when I try to run emirge.py, I get

2/27/19

Cyrus Zhou, Ajit Kumar Patra2

2/20/19

Hi Cyrus Z, I got an error the same as yours. I hope you solved this error. Could you please tell me,

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Hi Cyrus Z, I got an error the same as yours. I hope you solved this error. Could you please tell me,

2/20/19

david....@googlemail.com, spongebob2

2/20/19

Failure during iterations

Hi david, Did you ever solve this? I have the same issue myself. On Monday, November 28, 2016 at 3:24

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Failure during iterations

Hi david, Did you ever solve this? I have the same issue myself. On Monday, November 28, 2016 at 3:24

2/20/19

reb.g...@gmail.com

1/31/19

Partial gene reconstruction

Hi Chris, Is there a way to configure the EMIRGE command to assemble partial SSU rRNA gene sequences?

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Partial gene reconstruction

Hi Chris, Is there a way to configure the EMIRGE command to assemble partial SSU rRNA gene sequences?

1/31/19

r.mo...@gmail.com, … Drishti Kaul3

10/16/18

failure to align any reads on iteration 4

Hi! I got the same error for one out of my 27 samples, and it seems like the values for mean insert

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failure to align any reads on iteration 4

Hi! I got the same error for one out of my 27 samples, and it seems like the values for mean insert

10/16/18

8/26/18

Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

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Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

8/26/18

anferneeb...@gmail.com

7/11/18

EMIRGE error (very new)

Greetings, I have been getting the following errors when running EMIRGE on some paired end

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EMIRGE error (very new)

Greetings, I have been getting the following errors when running EMIRGE on some paired end

7/11/18

mariarovis...@gmail.com

5/13/18

EMIRGE ERROR - using EMIRGE with Phyloflash

Good morning, I am trying to extract 16S sequences to get my taxonomical profiles using the program

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EMIRGE ERROR - using EMIRGE with Phyloflash

Good morning, I am trying to extract 16S sequences to get my taxonomical profiles using the program

5/13/18

12/9/17

understanding EMIRGE output data

Dear Miller, First of all, I would like to thank you for developing such a user-friendly tool (EMIRGE

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understanding EMIRGE output data

Dear Miller, First of all, I would like to thank you for developing such a user-friendly tool (EMIRGE

12/9/17

10/18/17

EMIRGE tutorial

Hello EMIRGE developers, I came across with EMIRGE publications (doi:10.1186/gb-2011-12-5-r44 and

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EMIRGE tutorial

Hello EMIRGE developers, I came across with EMIRGE publications (doi:10.1186/gb-2011-12-5-r44 and

10/18/17

Lauren, … ltom.b...@gmail.com10

7/28/17

help installing EMIRGE

Hi Chris, I got (40) 16S taxa as output from EMIRGE (using the default SILVA reference database). For

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help installing EMIRGE

Hi Chris, I got (40) 16S taxa as output from EMIRGE (using the default SILVA reference database). For

7/28/17

Chris Miller, … Beatrice Garcia Rodriguez8

7/17/17

Re: install error

Good to hear it is fixed. Thanks for reporting back. On Thursday, July 13, 2017 at 5:54:50 PM UTC-6,

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Re: install error

Good to hear it is fixed. Thanks for reporting back. On Thursday, July 13, 2017 at 5:54:50 PM UTC-6,

7/17/17

debji...@gmail.com, Chris Miller2

7/12/17

problem in emirge

Debjit, It looks like you need to specify that you have 33-based quality encoding. Try adding --

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problem in emirge

Debjit, It looks like you need to specify that you have 33-based quality encoding. Try adding --

7/12/17

6/5/17

Emirge 16S reconstrution and QIIME

Hi, I trying to use the Emirge for amplicon of 16S and the QIIME for define the OTUs. I would like to

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Emirge 16S reconstrution and QIIME

Hi, I trying to use the Emirge for amplicon of 16S and the QIIME for define the OTUs. I would like to

6/5/17

soniat, … manue...@gmail.com3

4/4/17

general questions/notes about emirge output

Hi Chris, Could you please confirm that nowhere do you get information in the EMIRGE output as to how

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general questions/notes about emirge output

Hi Chris, Could you please confirm that nowhere do you get information in the EMIRGE output as to how

4/4/17

xue....@gmail.com

2/27/17

[fai_load] fail to open FASTA index for the iteration 4

Hi, I meet a very strange error when running EMIRGE when performing the iteration step. At the first

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[fai_load] fail to open FASTA index for the iteration 4

Hi, I meet a very strange error when running EMIRGE when performing the iteration step. At the first

2/27/17

bouchra...@gmail.com

2/27/17

Hi, I just started using Emirge and would like to know what the input files should look like. Thanks

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Hi, I just started using Emirge and would like to know what the input files should look like. Thanks

2/27/17

Chris Miller, … jincheng...@gmail.com4

2/27/17

New way to build a default candidate SSU database for EMIRGE

I am not the developer but I think your error is due to vsearch. Have you installed vsearch? You can

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New way to build a default candidate SSU database for EMIRGE

I am not the developer but I think your error is due to vsearch. Have you installed vsearch? You can

2/27/17

Chris Miller, … sker...@gmail.com8

1/9/17

Re: Usearch not found when in fact in path

Hello: I seem to have a similar issue to a previous post about not being able to find usearch,

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Re: Usearch not found when in fact in path

Hello: I seem to have a similar issue to a previous post about not being able to find usearch,

1/9/17

nkwell...@gmail.com

12/12/16

Error while gzip probN.pkl.gz

Hello, I encountered an error which seemed like to be related to gzip in the process. Could you help

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Error while gzip probN.pkl.gz

Hello, I encountered an error which seemed like to be related to gzip in the process. Could you help

12/12/16

7/20/16

EMIRGE error - too few reads?

Hi Chris, I was having a whirl at running EMIRGE on a relatively low coverage surface ocean dataset.

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EMIRGE error - too few reads?

Hi Chris, I was having a whirl at running EMIRGE on a relatively low coverage surface ocean dataset.

7/20/16

Roxanne Beinart

6/30/16

ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pysam/libchtslib.so, 2): Symbol not found: _hfile_plugin_init_libcurl

Hello, I installed Emirge successfully (no errors for build and for install) but am getting the below

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ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pysam/libchtslib.so, 2): Symbol not found: _hfile_plugin_init_libcurl

Hello, I installed Emirge successfully (no errors for build and for install) but am getting the below

6/30/16

blake...@gmail.com, … Dylan Bodington5

5/30/16

Exporting EMIRGE data to a QIIME usable format

If anyone is interested in using EMIRGE with QIIME, I've posted my modded scripts. On Monday, 30

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Exporting EMIRGE data to a QIIME usable format

If anyone is interested in using EMIRGE with QIIME, I've posted my modded scripts. On Monday, 30

5/30/16

Galen Seilis, xulin...@gmail.com4

4/14/16

IOError: could not open file `/.../EMIRGE_output/iter.00/iter.00.cons.fasta`

Hi Ling, Sure, as best as I can recall, I didn't have permission to execute emirge_amplicon.py.

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IOError: could not open file `/.../EMIRGE_output/iter.00/iter.00.cons.fasta`

Hi Ling, Sure, as best as I can recall, I didn't have permission to execute emirge_amplicon.py.

4/14/16

James Doonan, … xulin...@gmail.com6

4/13/16

fail to open fasta index

Hi Chris, I met the same error as James. Here is the error report: I don't know what to do, I

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fail to open fasta index

Hi Chris, I met the same error as James. Here is the error report: I don't know what to do, I

4/13/16

xue....@gmail.com, Chris Miller2

4/9/16

ImportErrors of 'gzread' when running 'emirge_amplicon.py'

For anyone with the same error, this has been addressed here: https://github.com/csmiller/EMIRGE/

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ImportErrors of 'gzread' when running 'emirge_amplicon.py'

For anyone with the same error, this has been addressed here: https://github.com/csmiller/EMIRGE/

4/9/16

gina...@gmail.com, … Chris Miller8

2/10/16

[None for x in range(max(self.sequence_name2sequence_i[-1].values())+1)]

Well that's confusing! So what are the 682 mappings reported in the log? You can send the bam

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[None for x in range(max(self.sequence_name2sequence_i[-1].values())+1)]

Well that's confusing! So what are the 682 mappings reported in the log? You can send the bam

2/10/16

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