the same problem
How can I (we) replace the goBambus2.py?
thank you in advance.
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Hi rahularjun86 I have the same problem that you had. The error on line 364. I checked goBambus2.py agains the script that is in the link that maubp gave. I found that there is an extra %s on line 364. Do you think this is the problem?
I cannot change the script because I have no experience with Python. And I want to replace the file as you did. How did you replace it? I installed mine with the amos package -3.1.0, where can I find the correct file? What are the other things that you reinstalled?
Thank you in advance
NAdia
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Hi maubp,
I have been trying to run the goBambus from Amos package and I was hitting at this error:
File "/opt/amos-3.1.0/bin/goBambus2.ori", line 364
scafffile = open("%s.scaffold.linear.fasta"%(outprefix), 'w')
^
IndentationError: unindent does not match any outer indentation level
I tried to put your code above and run it , but still I am not able to run it because of the below error:
goBambus2_1 contigs_mixed.fasta myscaff --all --contigs
/opt/amos-3.1.0/bin/goBambus2_1: line 4: import: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 6: RED: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 7: GREEN: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 8: BLUE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 9: NONE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 12: AMOSDIR: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 13: LOGFILE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 16: syntax error near unexpected token `('
/opt/amos-3.1.0/bin/goBambus2_1: line 16: ` logfile = open(LOGFILE,'w')'
Minimus2]$ goBambus2_1 -c contigs_mixed.fasta -o out
/opt/amos-3.1.0/bin/goBambus2_1: line 4: import: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 6: RED: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 7: GREEN: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 8: BLUE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 9: NONE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 12: AMOSDIR: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 13: LOGFILE: command not found
/opt/amos-3.1.0/bin/goBambus2_1: line 16: syntax error near unexpected token `('
/opt/amos-3.1.0/bin/goBambus2_1: line 16: ` logfile = open(LOGFILE,'w')
Can you help me to troubleshoot it?
Satish
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Dear maubp,
Bambus2 is running successfully on my machine now. But I am confused regarding the input files for bambus. what is the mate file and how to generate it? I have .contig file from minimus2 run.
Is this mate file I need to generate from the Illumina paired-end data I assembled using velvet??? Please share your experience
Regards,
Rahul
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Hi, I just replace the goBambus2.py file and reinstall the things and it is working now
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The indentation as shown in the forum post is certainly inconsistent - even allowing for missing white space at the very start for the first line. This seems to be the latest version,
Here by eye in the browser the indentation looks OK at line 364. One guess is there could be a mixture of tabs and spaces which is best avoided (the Python style guide says use just spaces).
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Thanks for your reply. I am using amos tools (http://sourceforge.net/projects/amos/files/amos/3.1.0/). Also trying to install Bambus2 separately, but it is also not working.
Code is following:
Code:p = subprocess.Popen(AMOSDIR+"Linearize -b %s"%(amosbank), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) if xopt_dict["verbose"] == 1: print "9) running Linearize" else: print "9) running Linearize...", sys.stdout.flush() sts = os.waitpid(p.pid,0)[1] if xopt_dict["verbose"] != 1: if sts == 0: print "\t\t%s...success!%s"%(GREEN,NONE) else: print "\t\t%s...failed%s"%(RED,NONE) sys.exit(1) p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) if xopt_dict["verbose"] == 1: print "10) running OutputResults" else: print "10) running OutputResults...", sys.stdout.flush()
Rahul
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Looks like a white space indentation problem in the Python script.
Can you copy and past the region of code at line 364 and paste it here inside a [ code ] and [ /code ] block? Say lines 350 to 370 would do?
Or if you know exactly which version of goBambus you have, can you give a URL for the source file?
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Bambus2 error
Hi all,
I am getting following error while running goBambus2 for scaffolding.
HTML Code:File "/home/rsharma/Software/amos-3.1.0/bin/goBambus2", line 364 p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ^ IndentationError: unindent does not match any outer indentation level
Regards,
RahulTags: None
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