only this file size ~200k
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I just tried v.1.1.1. No problems.
What is this addition (--wrapper basic-0) to the command line you are using?Comment
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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 plasmidsComment
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I am not seeing (--wrapper basic-0) in the log output from the build process anywhere.Comment
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yes, like I say, that only comes up in the error I get.Comment
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I can only think its something to do with my available ram and the way bowtie splits files.. a bad coincidence maybe..Comment
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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.Comment
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I am waiting to hear from our server admin to see if we can try some other configuration.Comment
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I remember you saying somewhere in this thread that you had 80G so that should not be an issue.Originally posted by susanklein View PostComment
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thanks i will try bbmapComment
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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.Comment
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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