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Old 08-15-2013, 11:39 AM   #1
illinu
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Default Contig Integrator for Sequence Assembly (CISA) error

Hi,

I am trying CISA program to integrate a set of contigs obtained with different assemblers and it seems pretty easy to run. Just 2 python scritps, one to merge the contigs and the second to perform the integration but so far I am getting this error:

python CISA.py cisa.config
CISA1....
Contigs: 887
Whole_Genome: 0
Ref0.fa and Query0.fa start to run NUCmer!
Done!
Traceback (most recent call last):
File "CISA.py", line 34, in <module>
my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
File "/home/Documents/Software/CISA1.2/src/CISA1/Controllor_R1.py", line 43, in Start
mywork.Start(genome_l,infile,nucmer)
File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 172, in Start
self.make_new_coords()
File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 87, in make_new_coords
f=open('CISA1/result'+str(count)+'.coords')
IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'


Anyone knows what's wrong? There isn't any prework specifying anything about that result0.coords file.

Thanks
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Old 08-15-2013, 11:45 AM   #2
illinu
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I just tried this program in Centos and I got a different error:

python CISA.py cisa.config
Traceback (most recent call last):
File "CISA.py", line 31, in <module>
from Controllor_R1 import R1
ImportError: No module named Controllor_R1
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Old 10-21-2013, 07:26 PM   #3
Yue Xu
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Quote:
Originally Posted by illinu View Post
I just tried this program in Centos and I got a different error:

python CISA.py cisa.config
Traceback (most recent call last):
File "CISA.py", line 31, in <module>
from Controllor_R1 import R1
ImportError: No module named Controllor_R1
Hi, illinu, I have met the same as your. Do you sovle it?

yours sicerely,
Yue Xu
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Old 10-22-2013, 03:19 AM   #4
illinu
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Hi Yue Xu,
Yes! I contacted the owners and they explained that the only reason CISA can go wrong is due to not specifying the correct paths in the config file. I searched all the programs (nucmer, ncbi, etc) with 'which' command and copied the path. Then it worked.

Hope it helps
Illinu
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Old 10-22-2013, 03:41 AM   #5
Yue Xu
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Hi illinu,
Thank your reply. I also can run it.

Best wishes,
Yue Xu
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Old 06-04-2014, 03:38 PM   #6
eyeziko
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Default CISA answer

Hi,

I am trying CISA program to integrate a set of contigs obtained with different assemblers and it seems pretty easy to run. Just 2 python scritps, one to merge the contigs and the second to perform the integration but so far I am getting this error:

python CISA.py cisa.config
CISA1....
Contigs: 887
Whole_Genome: 0
Ref0.fa and Query0.fa start to run NUCmer!
Done!
Traceback (most recent call last):
File "CISA.py", line 34, in <module>
my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
File "/home/Documents/Software/CISA1.2/src/CISA1/Controllor_R1.py", line 43, in Start
mywork.Start(genome_l,infile,nucmer)
File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 172, in Start
self.make_new_coords()
File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 87, in make_new_coords
f=open('CISA1/result'+str(count)+'.coords')
IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'


Anyone knows what's wrong? There isn't any prework specifying anything about that result0.coords file.

Thanks

Hello, I am just wondering if you were able to solve the problem. I ran into the same problem as above with CISA and I am yet to find a solution. Will appreciate your answer. Thank you
eyeziko

Last edited by eyeziko; 06-04-2014 at 03:39 PM. Reason: forgot to include original question
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Old 06-05-2014, 12:16 AM   #7
illinu
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Quote:
Originally Posted by eyeziko View Post
Hi,
Hello, I am just wondering if you were able to solve the problem. I ran into the same problem as above with CISA and I am yet to find a solution. Will appreciate your answer. Thank you
eyeziko
Hello eyeziko, My answer above to Yue Xu explains how I got it working:

Quote:
Hi Yue Xu,
Yes! I contacted the owners and they explained that the only reason CISA can go wrong is due to not specifying the correct paths in the config file. I searched all the programs (nucmer, ncbi, etc) with 'which' command and copied the path. Then it worked.
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Old 06-10-2014, 01:14 PM   #8
eyeziko
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Thank you. it did work.
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Old 11-21-2014, 08:18 AM   #9
chariko
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Quote:
Originally Posted by Yue Xu View Post
Hi illinu,
Thank your reply. I also can run it.

Best wishes,
Yue Xu
I am having the same problem but after putting the way after running the command which it continues not working.

Thatśs my CISA config file:

genome=7000000
infile=1D14_Merged.ctg.fa
outfile=1D14_CISA.ctg.fa
nucmer=/usr/bin/nucmer
R2_Gap=0.95
CISA=/home/user/Illumina/software/CISA1.3/CISA.py
makeblastdb=/usr/bin/makeblastdb
blastn=/usr/bin/blastn

Any clue?

Thanks in advance
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Old 11-21-2014, 08:20 AM   #10
illinu
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Yes, change
CISA=/home/user/Illumina/software/CISA1.3/CISA.py
for
CISA=/home/user/Illumina/software/CISA1.3
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Old 11-21-2014, 08:32 AM   #11
chariko
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Quote:
Originally Posted by illinu View Post
Yes, change
CISA=/home/user/Illumina/software/CISA1.3/CISA.py
for
CISA=/home/user/Illumina/software/CISA1.3
Thank you very much for your comment. I did it and now I got the following error:

CISA.config
CISA1....
Contigs: 2013
Whole_Genome: 0
Ref0.fa and Query0.fa start to run NUCmer!
Done!
Traceback (most recent call last):
File "/home/user/Illumina/software/CISA1.3/CISA.py", line 34, in <module>
my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Controllor_R1.py", line 43, in Start
mywork.Start(genome_l,infile,nucmer)
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 172, in Start
self.make_new_coords()
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 87, in make_new_coords
f=open('CISA1/result'+str(count)+'.coords')
IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'

In theory this error is due to the wrong path for nucmer as told in troubleshooting but I do not know why am I getting that error.

If I run nucmer (it's on the path) it runs normally so I don know what's happening

Thanks again
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Old 11-21-2014, 08:38 AM   #12
illinu
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Did you get the paths to nucmer with
$ which nucmer

I have it in /usr/bin/nucmer but you might have it elsewhere... check that well. Check it for all.

Also make sure you write
CISA=/home/user/Illumina/software/CISA1.3
and not
CISA=/home/user/Illumina/software/CISA1.3/

remove the last '/'
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Old 11-21-2014, 08:58 AM   #13
chariko
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Quote:
Originally Posted by chariko View Post
Thank you very much for your comment. I did it and now I got the following error:

CISA.config
CISA1....
Contigs: 2013
Whole_Genome: 0
Ref0.fa and Query0.fa start to run NUCmer!
Done!
Traceback (most recent call last):
File "/home/user/Illumina/software/CISA1.3/CISA.py", line 34, in <module>
my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Controllor_R1.py", line 43, in Start
mywork.Start(genome_l,infile,nucmer)
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 172, in Start
self.make_new_coords()
File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 87, in make_new_coords
f=open('CISA1/result'+str(count)+'.coords')
IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'

In theory this error is due to the wrong path for nucmer as told in troubleshooting but I do not know why am I getting that error.

If I run nucmer (it's on the path) it runs normally so I don know what's happening

Thanks again
I could finally run the program when I put all my files in the CISA1.3 folder. I still don't know why it does not work in their original folder but at least it worked.

Thanks a lot
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