Bambus2 error

[felipelira3]

the same problem

How can I (we) replace the goBambus2.py?
thank you in advance.

[NAdia1234]

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

[satishkumar]

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

[maubp]

I've never used Bambus2 so I can't help you - sorry.

[rahularjun86]

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

[rahularjun86]

Hi, I just replace the goBambus2.py file and reinstall the things and it is working now

[maubp]

Many thanks,, It is working now

What changed? Or what did you change - is there a bug AMOS need to fix?

[rahularjun86]

Many thanks,, It is working now
Thanks,
Rahul

[maubp]

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,

http://amos.git.sourceforge.net/git/gitweb.cgi?p=amos/amos;a=blob;f=src/Pipeline/goBambus2.py;h=a9120c397da6fc6f2b285ecb4dc227f9407bcd40;hb=HEAD

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).

[rahularjun86]

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:

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()

Thanks,
Rahul

[maubp]

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?

[rahularjun86]

Hi all,
I am getting following error while running goBambus2 for scaffolding.

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

Do anyone have any idea how to fix this? I would really appreciate your response.

Regards,
Rahul