Dear Galaxy Community,
I have a local instance and installed 0.5.9-r16 BWA and the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on the
sam file from the alignment, but it spits out this error:
*Dataset 26: Filter SAM on data 24*
Tool execution generated the following error message:
Traceback (most recent call last):
File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 148, in <module>
if __name__ == "__main__": main()
File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 137, in main
flags = int( fields[flag_col] )
ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433'
I have the same workflow online and did the exact same steps on the same
fastq files.
Is there anything I am missing? Is there any information I can provide to
answer this question?
Best
Moritz
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