Merging of contigs files by minimus2

Question

[waqasnayab]

Hi,

I am following the link: http://amos.sourceforge.net/wiki/index.php/Minimus2

for the merging of two contig files from velvet. It is written on the link: "......for merging one or two sequence sets (S1,S2)." here, do sequence sets mean contig files in fasta format?

I am facing the following error during merging:

command is:

./minimus2 all_velvet -D REFCOUNT=213048

error:

The log file is: all_velvet.runAmos.log
Doing step 10:  Building AMOS bank & Dumping reads
Doing step 11
Doing step 12
Doing step 13
Doing step 20:  Getting overlaps
Doing step 21
Command: /usr/bin/show-coords -H -c -l -o -r -I 94 all_velvet.delta | /home/kamran/Desktop/amos-3.1.0/bin/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > all_velvet.coords  exited with status: 1

Help required

Regards,
Waqas

[gangireddy]

I think there may be no over lapping sequences to connect

Answer 1

[JV]

I know this post is OLD. Just answering anyway, in case anybody else has problems with this.

I got the same error message when testing minimus2 recently, and it turns out this was NOT because no overlaps would be detected (would have hoped for a more informative message on that, anyway). Turns out, the standard error-output of minimus2 is not very helpful. You have to check the ".runAmos.log" file for actual info on what went wrong. (in your case that would be "all_velvet.runAmos.log".

In my case I found that minimus was expecting the tools delta-filter and show-coords at /usr/local/bin. However this may not be the case if you installed amos locally on a shared server, where you have no admin rights (as I did via bioconda).

Therefore you may have to manually edit the minimus2 script at lines 46 & 47 to point to the correct executables. Solved the problem for me!

[waqasnayab]

But still Thanksssss