Macs14 - Invalid Literal for int error
Hi guys, (Sorry for showing up on this list so much, hopefully I'll get everything running soon!) On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg we get this error: Dataset generation errors Dataset 74: MACS14 on data 29 and data 24 (peaks: bed) Tool execution generated the following error message: Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start'
Hello Greg It looks like you're running the version of the MACS14 tool from the toolshed? I think we also ran into this here and I patched the macs14_wrapper.py thusly to work around it: diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py index ccefb10..c0cf099 100644 --- a/macs14/macs142_wrapper.py +++ b/macs14/macs142_wrapper.py @@ -37,7 +37,13 @@ def xls_to_interval( xls_file, interval_file, header = None ): else: fields = line.split( '\t' ) if len( fields ) > 1: - fields[1] = str( int( fields[1] ) - 1 ) + try: + # Try to convert 'start' to int and shift + fields[1] = str( int( fields[1] ) - 1 ) + except ValueError: + # Integer conversion failed so comment out + # "bad" line instead + fields[0] = "#%s" % fields[0] out.write( '\t'.join( fields ) ) out.close() I'm intending to feed this back to the tool authors once things got a bit quieter here. HTH, best wishes Peter On 26/02/13 15:52, greg wrote:
Hi guys,
(Sorry for showing up on this list so much, hopefully I'll get everything running soon!)
On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg
we get this error:
Dataset generation errors
Dataset 74: MACS14 on data 29 and data 24 (peaks: bed)
Tool execution generated the following error message:
Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start' ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Thanks Peter. I'm running it now after applying your fix. Any idea what the problem was? -Greg On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hello Greg
It looks like you're running the version of the MACS14 tool from the toolshed? I think we also ran into this here and I patched the macs14_wrapper.py thusly to work around it:
diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py index ccefb10..c0cf099 100644 --- a/macs14/macs142_wrapper.py +++ b/macs14/macs142_wrapper.py @@ -37,7 +37,13 @@ def xls_to_interval( xls_file, interval_file, header = None ): else: fields = line.split( '\t' ) if len( fields ) > 1: - fields[1] = str( int( fields[1] ) - 1 ) + try: + # Try to convert 'start' to int and shift + fields[1] = str( int( fields[1] ) - 1 ) + except ValueError: + # Integer conversion failed so comment out + # "bad" line instead + fields[0] = "#%s" % fields[0] out.write( '\t'.join( fields ) ) out.close()
I'm intending to feed this back to the tool authors once things got a bit quieter here.
HTH, best wishes
Peter
On 26/02/13 15:52, greg wrote:
Hi guys,
(Sorry for showing up on this list so much, hopefully I'll get everything running soon!)
On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg
we get this error:
Dataset generation errors
Dataset 74: MACS14 on data 29 and data 24 (peaks: bed)
Tool execution generated the following error message:
Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start' ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi Greg - the issue is that when the wrapper processes the Macs output, it attempts to turn the 2nd column of every non-comment line (the "start" field) into an integer (as an aside, it then also subtracts 1 from this value). Unfortunately the line starting "chr start end ..." isn't commented, so the integer conversion fails causing the error you saw. The patch just traps for the integer conversion error. HTH, best wishes, Peter On 27/02/13 19:16, greg wrote:
Thanks Peter. I'm running it now after applying your fix.
Any idea what the problem was?
-Greg
On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hello Greg
It looks like you're running the version of the MACS14 tool from the toolshed? I think we also ran into this here and I patched the macs14_wrapper.py thusly to work around it:
diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py index ccefb10..c0cf099 100644 --- a/macs14/macs142_wrapper.py +++ b/macs14/macs142_wrapper.py @@ -37,7 +37,13 @@ def xls_to_interval( xls_file, interval_file, header = None ): else: fields = line.split( '\t' ) if len( fields ) > 1: - fields[1] = str( int( fields[1] ) - 1 ) + try: + # Try to convert 'start' to int and shift + fields[1] = str( int( fields[1] ) - 1 ) + except ValueError: + # Integer conversion failed so comment out + # "bad" line instead + fields[0] = "#%s" % fields[0] out.write( '\t'.join( fields ) ) out.close()
I'm intending to feed this back to the tool authors once things got a bit quieter here.
HTH, best wishes
Peter
On 26/02/13 15:52, greg wrote:
Hi guys,
(Sorry for showing up on this list so much, hopefully I'll get everything running soon!)
On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg
we get this error:
Dataset generation errors
Dataset 74: MACS14 on data 29 and data 24 (peaks: bed)
Tool execution generated the following error message:
Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start' ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Peter Briggs