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insert size error? #3

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 

I am trying to assemble the test phiX using a Linux Supercomputer system.  

I works good until it creates the xx.contigs.fasta file and then it appear to 
stop.  The end of the output looks like this:

[bwa_aln_core] 3128 sequences have been processed.
[a5] java -jar GetInsertSize.jar test.out.raw1.sub.pe.sam
The java class could not be loaded. java.lang.UnsupportedClassVersionError: 
(org/halophiles/assembly/InsertSizeExporter) bad major version at offset=6
Use of uninitialized value $ins_n in numeric gt (>) at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1493, 
<IN> line 2.
Use of uninitialized value $ins_n in concatenation (.) or string at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1499, 
<IN> line 2.
[a5] Discarding estimate. Not enough data points: 
Use of uninitialized value $ins_mean in multiplication (*) at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1500, 
<IN> line 2.
Use of uninitialized value in concatenation (.) or string at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1145, 
<IN> line 2.
Use of uninitialized value in concatenation (.) or string at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1145, 
<IN> line 2.
[a5] Printing preprocessed library file to test.out.preproc.libs
[a5] Processed libraries:
     raw1:
      id=raw1
      p1=phiX_p1.fastq.pp.ec.fastq
      p2=phiX_p2.fastq.pp.ec.fastq
      ins=0
      err=0
      nlibs=1
      libfile=test.out.library_1.txt
[a5_s3] Scaffolding contigs from test.out.contigs.fasta with SSPACE
[a5_s3] Scaffolding contigs from test.out.contigs.fasta with SSPACE
[a5] Total contig length 5469
[a5] raw1: Insert 0, coverage 49.20, expected links 0
Can't take log of 0 at 
/home/uahlmm/ngopt_a5pipeline_linux-x64_20120518/bin/a5_pipeline.pl line 1426, 
<READFILE> line 12516.

Is it appears that there is an error on how it calculates the insert size.  Is 
it something that needs to be install on the machine?

thank you

luciano

Original issue reported on code.google.com by lmm0...@uah.edu on 7 Oct 2012 at 8:24