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mozack / abra

Assembly Based ReAligner
MIT License
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[fwrite] Remote I/O error #24

Open bcantarel opened 8 years ago

bcantarel commented 8 years ago

I am running Abra-0.96 using abra-0.96-SNAPSHOT-jar-with-dependencies.jar

It runs over 24 hours and gives me the following error:

Clock time in Align and clean contigs: 49461 Sat Dec 19 21:10:43 CST 2015 : Indexing contigs Running: [bwa index -a bwtsw /qbrc/home/bcantarel/scratch/abra_temp_S2/clean_contigs.fasta] [bwa_index] Pack FASTA... [fwrite] Remote I/O error Stream thread done. Stream thread done. BWA time: 1313 seconds. Exception in thread "main" java.lang.RuntimeException: BWA exited with non-zero return code : [1] for command: [bwa index -a bwtsw /qbrc/home/bcantarel/scratch/abra_temp_S2/clean_contigs.fasta] at abra.Aligner.runCommand(Aligner.java:76) at abra.Aligner.runCommand(Aligner.java:33) at abra.Aligner.index(Aligner.java:103) at abra.ReAligner.alignReads(ReAligner.java:396) at abra.ReAligner.reAlign(ReAligner.java:214) at abra.ReAligner.run(ReAligner.java:1240) at abra.Abra.main(Abra.java:12)

When I try to run this command directly, I have the error: [bwa_index] unknown algorithm: 'bwtsq'.

Is there a way for me to run the indexing and not have abra start over at the beginning? Also looks like this indexing command is from a previous bwa version, is it possible to update? I couldn't compile on my system, hence I am using the precompiled version.

mozack commented 8 years ago

BWA is not compiled into ABRA. Rather, it uses the version that is in your command PATH. What version do you have in your path?

bcantarel commented 8 years ago

Oh, I see, there is a "global" install of 0.7.9 but I use a local install -- of 0.7.12 -- I guess my comment want that the command bwa index -a bwtsw does not work for all versions of bwa...
Also, I wanted to know if there is a way for me to run the indexing continue with the rest of the steps and not have abra start over at the beginning?

mozack commented 8 years ago

Sorry, I don't currently have a way to do that - short of modifying the code. That is an unusually long run time. Can you provide a line count of the index?

In the working dir run: wc -l clean_contigs.fasta

bcantarel commented 8 years ago

255611210

mozack commented 8 years ago

That is too many contigs and is unlikely to complete with the supported BWA version.

I suggest retrying with more aggressive graph pruning. i.e.

--mnf 5 --mbq 150