Hi all,
I've been trying to run Stampy 1.0.20 on a BAM file (produced by BWA) that has aligned some Illumina paired-end reads, but it is getting an error. I ran the following commands to build the index, build the hash, and re-align the BAM file:
python2.6 stampy.py --species=human -G hg37 human_g1k_v37.fasta
python2.6 stampy.py -g hg37 -H hg37
python2.6 stampy.py -g hg37 -h hg37 --solexa --bamkeepgoodreads -M xaa.bam > xaa.stampy.sam
The first two steps seem to succeed, but on the last step I get the following error:
stampy: Mapping...
stampy: Internal problem: File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/reader.py", line 1243, in generator
stampy: Internal problem: ZeroDivisionError('float division',)
stampy: Please report this problem to <[email protected]> mentioning the version number (1.0.20 (r1642)) and command line - thanks!
The resulting output xaa.stampy.sam file is empty. It says I can contact Gerton Lunter, but before doing so, I wanted to check if I was doing anything obviously wrong. (I would also look into the reader.py file, but I'm not sure where to find it). If anyone has any thoughts, please let me know. Thanks!
-Henry
I've been trying to run Stampy 1.0.20 on a BAM file (produced by BWA) that has aligned some Illumina paired-end reads, but it is getting an error. I ran the following commands to build the index, build the hash, and re-align the BAM file:
python2.6 stampy.py --species=human -G hg37 human_g1k_v37.fasta
python2.6 stampy.py -g hg37 -H hg37
python2.6 stampy.py -g hg37 -h hg37 --solexa --bamkeepgoodreads -M xaa.bam > xaa.stampy.sam
The first two steps seem to succeed, but on the last step I get the following error:
stampy: Mapping...
stampy: Internal problem: File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/reader.py", line 1243, in generator
stampy: Internal problem: ZeroDivisionError('float division',)
stampy: Please report this problem to <[email protected]> mentioning the version number (1.0.20 (r1642)) and command line - thanks!
The resulting output xaa.stampy.sam file is empty. It says I can contact Gerton Lunter, but before doing so, I wanted to check if I was doing anything obviously wrong. (I would also look into the reader.py file, but I'm not sure where to find it). If anyone has any thoughts, please let me know. Thanks!
-Henry
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