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Old 06-08-2011, 03:30 AM   #10
Himalaya
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Location: uk

Join Date: Jun 2010
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Quote:
Originally Posted by Jose Blanca View Post
I would need more information. A segmentation fault is quite a strange error in a python program. could you send me the output?
Hi Jose
I am using mac os snow leopard. My commandline is: clean_reads -i Pair01.fastq -o ./clean_reads/output_q20_len50_only3end -p 454 -f fastq -g fastq -qual_threshold 20 -only_3_end True -min_len 50. It only gave me one line error 'segmentation fault' and says python quit unexpectedly in separate window with long error report. A small last part of error report is below:
0x7fff8507b000 - 0x7fff85131fff libobjc.A.dylib 227.0.0 (compatibility 1.0.0) <1960E662-D35C-5D98-EB16-D43166AE6A22> /usr/lib/libobjc.A.dylib
0x7fff85288000 - 0x7fff85446fff libicucore.A.dylib 40.0.0 (compatibility 1.0.0) <3D9313BF-97A4-6B65-E583-F6173E64C3C2> /usr/lib/libicucore.A.dylib
0x7fff8643f000 - 0x7fff86461ff7 libexpat.1.dylib 7.2.0 (compatibility 7.0.0) <7D173736-CBDF-F02F-2D07-B38F565D5ED4> /usr/lib/libexpat.1.dylib
0x7fff86462000 - 0x7fff864aaff7 libvDSP.dylib 268.0.1 (compatibility 1.0.0) <98FC4457-F405-0262-00F7-56119CA107B6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x7fff87df1000 - 0x7fff87df1ff7 com.apple.Accelerate 1.6 (Accelerate 1.6) <15DF8B4A-96B2-CB4E-368D-DEC7DF6B62BB> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff8846a000 - 0x7fff88544fff com.apple.vImage 4.0 (4.0) <B5A8B93B-D302-BC30-5A18-922645DB2F56> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff88545000 - 0x7fff88d4ffe7 libBLAS.dylib 219.0.0 (compatibility 1.0.0) <2F26CDC7-DAE9-9ABE-6806-93BBBDA20DA0> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <40DA878D-6D69-FEA3-398B-BBD80C9BFF46> /usr/lib/libSystem.B.dylib

Then i tried to run clean_reads in ubuntu with same command and gave me error:
IOError: [Errno 2] No such file or directory: 'ual_threshold'
i did specify any file 'ual_threshold'. That was option -qual_threshold' i specified.
any advice..please
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