SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
.tmap file from cuffcompare capricy Bioinformatics 1 09-12-2013 07:48 AM
TMAP errors lwhitmore Ion Torrent 1 08-26-2013 04:00 AM
TMAP issue zjiexin Ion Torrent 0 07-03-2013 08:57 AM
GMAP vs TMAP jordi Bioinformatics 0 01-03-2012 01:05 AM
EnsEMBL variant effect predictor standalone error ketan_bnf Bioinformatics 0 02-16-2011 08:05 PM

Reply
 
Thread Tools
Old 06-30-2015, 05:23 AM   #1
skbrimer
Member
 
Location: OP Kansas

Join Date: Mar 2014
Posts: 53
Default Standalone TMAP 3.4.1 error

Good Morning gang,

I have had, for the first time TMAP fail to put together some PGM reads for me. I do not blame the algorithm the data is not the best, but it is weird.

Below is the code I use to run and in the stats output I get stats [0.00,-nan,-nan,-nan,-nan,-nan] which I assume means there is no data. However when I use bwa samse and bwa mem I get mapped reads AND when I use TMAP vsw option I get mapped reads but the mapall function I get nothing.

Code:
sean@LEN320:~/Desktop/IBV/D1456/tmap$ tmap mapall -f ~/Desktop/templates/IBV_RefSeq.fasta -r ../raw_data/all_reads_no_host.fastq -n4 -v stage1 map1 map2 map3 > aln.sam
[tmap mapall] running with 4 threads (user set).
[tmap mapall] map1 will be run in stage 1.
[tmap mapall] map2 will be run in stage 1.
[tmap mapall] map3 will be run in stage 1.
[tmap mapall] reading in reference data.
[tmap mapall] 0.01/0.08 sec: reference data read in.
[tmap mapall] calculating maximum differences in map1 for stage 1.
[tmap mapall] 17bp reads will have at most 2 differences.
[tmap mapall] 38bp reads will have at most 3 differences.
[tmap mapall] 64bp reads will have at most 4 differences.
[tmap mapall] 93bp reads will have at most 5 differences.
[tmap mapall] 124bp reads will have at most 6 differences.
[tmap mapall] 157bp reads will have at most 7 differences.
[tmap mapall] 190bp reads will have at most 8 differences.
[tmap mapall] 225bp reads will have at most 9 differences.
[tmap mapall] setting the seed length to 10 in map3.
[tmap mapall] loading reads.
[tmap mapall] 0.04/0.12 sec: loaded 11128 reads.
[tmap mapall] processing reads.
[tmap mapall] 1.28/1.13 sec: processed 11128 reads.
[tmap mapall] 1.28/1.13 sec: stats [0.00,-nan,-nan,-nan,-nan,-nan].
[tmap mapall] loading reads.
[tmap mapall] 1.28/1.13 sec: loaded 0 reads.
[tmap mapall] 1.28/1.13 sec: cleaning up.
[tmap mapall] 1.30/1.15 sec: terminating successfully.
I do not mind that the mapping failed I was just more usurious on why it failed so I can learn more about how to best work the different data sets. I have attached a screen shoot from IGV showing the 4 different mappings. from top to bottome it is TMAP mapall, TMAP mapvsw, BWA semse, BWA mem
Attached Images
File Type: jpeg tmap_failure.jpeg (135.6 KB, 5 views)
skbrimer is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO