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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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SNAP failed #204

Closed abshah closed 7 years ago

abshah commented 7 years ago

Hi Transrate users and developers,

I encounter a strange error with transrate version 1.0.3

[ INFO] 2016-10-25 15:51:02 : Contig metrics done in 55 seconds
[ INFO] 2016-10-25 15:51:02 : Calculating read diagnostics...
[ERROR] 2016-10-25 15:52:59 : Snap failed
Welcome to SNAP version 1.0dev.96.

Ran out of scoring candidate pool entries.  Perhaps trying with a larger value of -mcp will help.
SNAP exited with exit code 1 from line 490 of file SNAPLib/IntersectingPairedEndAligner.cpp

Is there a work around this or is there a way to pass arguments/flags to SNAP or salmon to get this to work ?

Best Wishes, Abhijeet

abshah commented 7 years ago

Hi Transrate users and developers,

I found a solution to this on the transrate users google group. You need to add this line between lines 39 and 40 cmd << " -mcp 10000000" # maximum candidate pool size to the file transrate-1.0.3-linux-x86_64/lib/app/lib/transrate/snap.rb

Best Wishes, Abhijeet