TMAP mapping for Ion Torrent

Question: TMAP mapping for Ion Torrent

3.7 years ago by

Argentina

Hi, I am installed TMAP from https://toolshed.g2.bx.psu.edu/view/nilshomer/tmap_wrapper in my local galaxy

I am trying to run TMAP using a reference sequence from my history, I uploaded the reference sequence as .fasta and selected a fastq file from the history also. Then for the setting I used "commanly used" but I found the following error

Tool execution generated the following error message:

Error indexing reference sequence. Warning: ambiguous qualifier f (fformat, fopenfile)

Warning: ambiguous qualifier 'f' (filter, fatal, fformat, fopenfile)

Died: Unknow qualifier -f

The tool produced the following additional output:

Could not determine TMAP version

I am also installed galaxy localy in my personal computer and installed TMAP for the same repository, and used the tool in the same conditions, and I have also problems, but the error is different.

Thanks for your help with TMAP!

Verónica

galaxy • 2.6k views

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modified 2.9 years ago by afaf.bioinfo • 0 • written 3.7 years ago by elmujtar.veronica • 30

Thanks Martin,

I will check the link of github to compile and install tmap

Veronica

ADD REPLY • link 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:

Hi Verónica,

the Galaxy Tool you installed does not define its dependencies through the Tool Shed, which means that it does not install the tmap tool itself automatically. You have to install it manualy on the machine that you want to run the Galaxy job on - in this case your laptop.

Details on how to compile and install tmap can be found here: https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

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

2.9 years ago by

afaf.bioinfo • 0

afaf.bioinfo • 0 wrote:

Hi,

I have had many troubles when trying to install TMAP as well but I have finished by running TMAP on my computer.

Installing TMAP:

Cloning a released version remains the best way to get a complete version of this tool, this can be done with the following commands:

$git clone git://github.com/iontorrent/TMAP.git
$cd TMAP
$git submodule init
$git submodule update

The update command above aims to add the last version of Samtools to the repository and eventually update the configuration's file.

To compile the TMAP you need to type:

$sh autogen.sh && ./configure && make

Then execute the command to install it:

$make install

Example of use:

First you need to index the reference fasta file:

$tmap index -f sequence.fasta

Then, enter the needed options to map your reads in reads.fastq to the reference indexed sequence sequence.fasta :

$tmap mapall -n 24 -f sequence.fasta -r reads.fastq -v -Y -u -a 3 -s result.sam -o 0 stage1 map4

mapall: command to perform mapping

map4: algorithm which is a variation of the super-maximal exact matching algorithm.

The output result.sam is in SAM format.

Problems than can be faced:

- The cloning from github doesn't work. This can be explained by a problem related to the internet connection quality. Try again with better mode of connection.

- Error message ' Segmentation fault (core dumped) ' . This problem can be settled by passing to mode Sudo when executing the command tmap.

ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by afaf.bioinfo • 0

Hello, may I ask you how had you fixed other troubles during TMAP installation ? Thanks

ADD REPLY • link written 10 days ago by theonly_f • 0

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Installing TMAP:

Example of use:

Problems than can be faced:

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