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Qualimap bamQC terminates with ArrayIndexOutOfBoundsException when to many reads. This issue should be fixed in latest version of Qualimap 2.0
`java.lang.ArrayIndexOutOfBoundsException: -452499825
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When piper runs qualimap with e.g. this commandline:
```
/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap --java-mem-size=64G bamqc -bam /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/_14…
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Testing Piper, alignments run ok but qualimap fails with the error shown below
```
/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap --java-mem-size=64G bamqc -bam /apus/v1/a2010002_n…
vezzi updated
10 years ago
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Last Friday I tried to run Piper on the 6 samples recently generated using V4 technology.
All the data and analysis can be found here (it should be accessible by all members of group a2010002) :
```
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vezzi updated
10 years ago
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bsub -J "blade16-4-16.gsc.wustl.edu 22551 1391457001 10035 BioSamtools Error Rate /opt/gms/6ZIZ926/fs/6ZIZ926/info/build_merged_alignments/merged-alignment-blade16-4-16.gsc.wustl.edu-ssmith-25047-cc53…
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I noticed this error on the test box blade16-4-16.
ERROR: bam-errorrate version0.9 is not valid tool at /opt/gms/YBPD617/sw/genome/lib/perl/Genome/Model/Tools/BioSamtools/ErrorRate.pm line 62.
This …
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The following two steps (and possibly others) request 32Gb of memory:
BamQc - Collect Picard Metrics
BamQc - Collect Picard G+C Bias
Since this is more than the VM has, these steps enter a pending s…