Prettyprint and SHRiMP 2.2.2

[evilution84]

Hello,

I am having an issue with the pretty print function in SHRiMP 2.2.2.

I have several scripts for working through the pipeline (that work for 2.1.1b).

With 2.2.2, I use gmapper-cs, then some filtering, then use probcalc, and finally I want to use prettyprint-cs. However, I get this error:

Loading shrimp output file...
Loaded 11537 alignments from shrimp output (11537 unique reads)
Loading read file(s)...
Loaded 11537 colourspace reads in 1 file(s) (415332 total bases)
Loading genome contig file(s)...
warning: score differs from input file (read="862_925_542", genome="Bd1_100805_100840_F")
         Most likely cause is that prettyprint does not use anchors.
*** glibc detected *** double free or corruption (out): 0x000000000970fc80 ***
/share/sge6.2/execd_spool//i182-110/job_scripts/2376614: line 11:  1506 Aborted

I make sure to use the --shrimp-format flag for gmapper-cs. Anyone have any insights here? If I run gmapper with the -p flag it WILL prettyprint (but I need to do some more filtering before this step).

Appreciate it.

[evilution84]

Hmm you know what... never mind... I would just delete this post, but you may find this useful. The newest version of SHRiMP does not fix the terminal gaps issue, so it really gains us nothing (at least for my purposes). Thus, we will continue to use version 2.1.1b