TMAP problems in galaxy

Question: TMAP problems in galaxy

3.7 years ago by

Argentina

Hi, I am installing TMAP in local galaxy, but when I run it using commonly settings I found the next error report

The alignment failed.
Error mapping sequence. 
src/map/mapall/tmap_map_all.c:175: in function "tmap_map_all_opt_parse"
No stages were specified
warning: command line argument
trying to continue...


 [31mtmap:    [37mtorrent mapper [0m
 [31mVersion:  [37m3.4.1 [0m  [31mgit: [37m39c56e6cd6471b8d796e3b8af2c00206f1002fae [0m
 [31mWeb Site:  [37mhttp://github.com/iontorrent/tmap [0m
 [31mContact:  [37mhttp://ioncommunity.lifetechnologies.com [0m

non-option command-line-elements:
fastq: unknown command line option
map1: recognized an algorithm name, did you forget to include the stage parameter?
map2: recognized an algorithm name, did you forget to include the stage parameter?
map3: recognized an algorithm name, did you forget to include the stage parameter?

Anyone know what is the problem?

I am installed the version

3.4.1 git:39c56e6cd6471b8d796e3b8af2c00206f1002fae

that is OK? or I need to install an older version?

Thanks!

tmap galaxy • 805 views

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modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by elmujtar.veronica • 30

3.7 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

The Galaxy Tool (in tmap_wrapper.py) states 'Works with TMAP version 0.0.19 or higher.'

However the latest version of tmap is 3.0.1 which is a major upgrade.

You have probably compiled the latest version and if the Galaxy Tool and tmap are incompatible (which might be true given the version difference) one of the two following routes should to be taken:

* update Galaxy Tool to work with the newest tmap (you can contact the owner of the toolshed repository, maybe he/she is interested in updating the Galaxy Tool for you - you can do so in the top right menu on this page:https://toolshed.g2.bx.psu.edu/view/nilshomer/tmap_wrapper )
* compile and use older tmap (start with version 0.1.19) and try running it with that

ADD COMMENT • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

Thanks Martin

I will try your recommendations!

ADD REPLY • link written 3.7 years ago by elmujtar.veronica • 30

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