[susanklein]

only this file size ~200k

[GenoMax]

I just tried v.1.1.1. No problems.

What is this addition (--wrapper basic-0) to the command line you are using?

[susanklein]

that is not my addition... that only comes out in the error message. I only used:
bowtie2-build plasmids.fna plasmids
or
bowtie-build plasmids.fna plasmids

[GenoMax]

I am not seeing (--wrapper basic-0) in the log output from the build process anywhere.

[susanklein]

yes, like I say, that only comes up in the error I get.

[susanklein]

I can only think its something to do with my available ram and the way bowtie splits files.. a bad coincidence maybe..

[GenoMax]

I would ask you to write to the authors of bowtie but chances of getting a response are slim.

If you are able to use a different program then I recommend BBMap. Give it a try. Simple to use and fast. Plus Brian (its author) participates actively on SeqAnswers.

[susanklein]

I am waiting to hear from our server admin to see if we can try some other configuration.

[GenoMax]

I can only think its something to do with my available ram and the way bowtie splits files.. a bad coincidence maybe..

I remember you saying somewhere in this thread that you had 80G so that should not be an issue.

[susanklein]

thanks i will try bbmap

[susanklein]

hmm.. bbmap doesn't work. Java. Hate java

$ ~/bin/bbmap/bbmap.sh ref=plasmids.fna
java -Djava.library.path=/OSM/HOME-MEL/all29c/bin/bbmap/jni/ -ea -Xmx33004m -cp /OSM/HOME-MEL/all29c/bin/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=plasmids.fna
Exception in thread "main" java.lang.UnsupportedClassVersionError: align2/BBMap : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:634)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: align2.BBMap. Program will exit.