[mjhsieh]

I wonder if there is a version LSC for Mac users.
Thanks

It should be runnable (through Terminal.app of course) after some minor modifications.

[joxcargator73]

I am using pacbio and illumina in a Novo-assembly. I am using the LSC to correct PacBio reads. Trying to edit the run.cfg. I wonder if somebody could clarify two options in the file:
lenght of pseudochromosomes (lpseudochr)
and length of gap sequence between long reads (LgapInpseudochr)?
Thanks

[cemonat]

Hi,
I'm using pacBio and illumina, and want to correct pacBio with LSC.
I create a WkgDir folder where I placed a bin folder with all binaries, and a data folder with my LR and SR sequences, I added run.cfg in WkgDir with the modified path.
I then launched the following command:

/ home / cecmonat / sources / LSC / runLSC.py run.cfg

and here are the errors that are returned :

['LR_pathfilename ', ' /data/projects/assembling-glab/PacBio_test/C2/filtered_subreads_C2.fasta']
['SR_pathfilename ', ' /data/projects/assembling-glab/SEQUENCES/TOG5681Clean/tog5681Clean_all.fasta']
['I_nonredundant ', ' N']
['Nthread1 ', ' 12']
['Nthread2 ', ' 12']
['temp_foldername ', ' /data/projects/assembling-glab/LSC_temp']
['output_foldername ', ' /data/projects/assembling-glab/LSC_out']
['Lpseudochr ', ' 50000000']
['LgapInpseudochr ', ' 100']
['I_RemoveBothTails ', ' Y']
['MinNumberofNonN ', ' 39']
['MaxN ', ' 1']
=== sort and uniq SR data ===
0:00:00.038417
===split SR:===
0:00:00.047578
===compress SR.aa:===
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
inseq=open(inseq_filename,'r')
IOError: [Errno 2] No such file or directory: '/data/projects/assembling-glab/LSC_temp/SR.fa.aa'
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
Traceback (most recent call last):
File "/home/cecmonat/sources/LSC/compressFASTA.py", line 52, in <module>
inseq=open(inseq_filename,'r')
inseq=open(inseq_filename,'r')
IOError: [Errno 2] No such file or directory: '/data/projects/assembling-glab/LSC_temp/SR.fa.ae'
inseq=open(inseq_filename,'r')
IOErrorIOError: inseq=open(inseq_filename,'r')
: [Errno 2] No such file or directory: '/data/projects/assembling-glab/LSC_temp/SR.fa.ac'[Errno 2] No such file or directory: '/data/projects/assembling-glab/LSC_temp/SR.fa.aj'

I do not know what the problem is ...
In the folder LSC_temp/ files there:

LR.fa.cps SR.fa.ag.cps.convertNAV.log
LR.fa.idx SR.fa.ah.cps.convertNAV.log
LR.fa.readname SR.fa.ai.cps.convertNAV.log
Notwotails_filtered_subreads_C2.fasta_intact_MS SR.fa.aj.cps.convertNAV.log
SR.fa.aa.cps.convertNAV.log SR.fa.ak.cps.convertNAV.log
SR.fa.ab.cps.convertNAV.log SR.fa.al.cps.convertNAV.log
SR.fa.ac.cps.convertNAV.log SR.fa.cps
SR.fa.ad.cps.convertNAV.log SR.fa.idx
SR.fa.ae.cps.convertNAV.log SR_uniq.fa
SR.fa.af.cps.convertNAV.log

but I do not know why there is an extension "cps.convertNAV.log" ... ?
Any idea ?
Thanks

[ashNZ]

Gday all,

I am trying to run LSC to improve my PacBio data to use for a hybrid de novo assembly of a cattle genome, however I am having trouble getting the program to run!
I am running Ubuntu 12.04, have installed Python 2.6 and when I go to run the program as per step 4 of the tutorial instructions on the LSC website I am getting this error:

bash: ./bin/runLSC.py: Permission denied

Anyone know why this is and how I can fix it??

Cheers
Ash

[winsettz]

ash,

The .py files don't have executable permissions.

For example, I use:

python /data4/Programs/LSC/LSC_023/runLSC.py run.cfg

I've yet to try setting it up with executable privileges, but that would be a

chmod u+x runLSC.py

to add (+) to the user (u) executable privileges (x).

I found an interesting indentation related error in LSC 023

def GetPathAndName(pathfilename):
    ls=pathfilename.split('/')
    filename=ls[-1]
    path='/'.join(ls[0:-1])+'/'
        if path == "/":
            path = "./"
    return path, filename

, which I had to fix by revising the indents to

def GetPathAndName(pathfilename):
    ls=pathfilename.split('/')
    filename=ls[-1]
    path='/'.join(ls[0:-1])+'/'
    if path == "/":
     path = "./"
    return path, filename

I get the feeling I'm the only one this happened to, but I'm just putting it out there.

It's worth noting that all the other python files have permission issues. You can give user-executable permissions to all the python files in LSC with

chmod u+x *.py

[ashNZ]

Cheers for your answer, it was very helpful. I've run into another problem I haven't been able to work out. After checking the parameters of my config file to make sure that all of the file paths are correct etc... when I run the program I am getting an error saying the program cannot find my .fa data files. It looks like this:

=== sort and uniq SR data ===
awk: cmd. line:1: fatal: cannot open file '/home/Bioinformatics/LSC/example/data/SR.fa' for reading (No such file or directory)
0:00:00.025276

I'm a little confused by this as the SR.fa file is at the path specified! Anyone know what the problem might be here?

Cheers
Ash

[winsettz]

What are the permissions of your SR.fa file? It's possible you may have stripped read permissions (-wx------). Unlikely, but...

[ashNZ]

Not sure....

What are the permissions of your SR.fa file? It's possible you may have stripped read permissions (-wx------). Unlikely, but...

I'm not sure... how can I check that? I am just using the example package from the 'tutorial' section of the LSC website

[winsettz]

===convertNAV SR.aa.cps.nav:===
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
IndexError: list index out of range
start_pt = int(line_list[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
start_pt = int(line_list[3])
start_pt = int(line_list[3])
IndexError: list index out of range
IndexError: list index out of range
IndexError: list index out of range
start_pt = int(line_list[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
IndexError: list index out of range
start_pt = int(line_list[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/data4/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/data4/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
start_pt = int(line_list[3])
IndexError: list index out of range
start_pt = int(line_list[3])
IndexError: list index out of range
6:12:15.153565
===merge_mapping_file SR.aa.cps.nav.map:===
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/merge_mapping_file.py", line 22, in <module>
LR_SR_mapping_file = open(LR_SR_mapping_filename,'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.aa.cps.nav.map'
6:12:15.434721
rm: cannot remove `temp/SR.fa.aa.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ab.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ac.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ad.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ae.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.af.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ag.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ah.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ai.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.aj.cps.nav.map': No such file or directory
rm: cannot remove `temp/SR.fa.ak.cps.nav.map': No such file or directory
===split LR_SR.map:===
rm: cannot remove `temp/SR.fa.al.cps.nav.map': No such file or directory
Traceback (most recent call last):
File "/data4/Programs/LSC/LSC_023/runLSC.py", line 326, in <module>
LR_SR_map = open(temp_foldername +"LR_SR.map",'r')
IOError: [Errno 2] No such file or directory: 'temp/LR_SR.map'

Looks like list index out of range borks everything up.

[winsettz]

to check permissions:

ls -la *.fa

-rw-r--r-- 1 user group 51109952 Aug 13 2012 LR.fa
-rw-r--r-- 1 user group 109888896 Aug 13 2012 SR.fa

[ashNZ]

Cheers! Had a look and the permissions are definitely fine, files are -rwxrwxrwx.... any other ideas on what it could be? I might try start from scratch, uninstall everything and then rebuild it all. The other thing I wanted to know is with regards to novoalign.... am I correct in the assumption that you can copy and paste the binaries into the same bin folder where the LSC binaries are located?

[winsettz]

Cheers! Had a look and the permissions are definitely fine, files are -rwxrwxrwx.... any other ideas on what it could be? I might try start from scratch, uninstall everything and then rebuild it all. The other thing I wanted to know is with regards to novoalign.... am I correct in the assumption that you can copy and paste the binaries into the same bin folder where the LSC binaries are located?

Don't need to.

PATH=/directory/for/novolign:$PATH

which novolign

/directory/for/novolign/novolign

I guess you could try delete and reinstall. Is your /usr/bin/python the one you intend to use, or some other local copy of python? If local copy you may want to change the headers to point to it.

[ashNZ]

Don't need to.

PATH=/directory/for/novolign:$PATH

which novolign

/directory/for/novolign/novolign

I guess you could try delete and reinstall. Is your /usr/bin/python the one you intend to use, or some other local copy of python? If local copy you may want to change the headers to point to it.

I guess that this may be contributing to the problem also... as I am running ubuntu 12.04 which comes with Python 2.7, so I am using a local copy of Python 2.6. Can you tell me where I need to edit the headers to point to LSC to my local copy and how I can do this?

Also, I understand the function of the novoalign command, but where do I need to add this? Sorry if these questions seem idiotic lol, I'm a rookie with regards to this stuff

Cheers
Ash

[winsettz]

If you're running this interactively, you'd have to add the PATH command to your .bashrc (not necessarily kosher, as one day you may have tons of stuff in your .bashrc that can conflict); or you can type it each time. If you're doing this in a batch script, you can put it in there.

which novolign is basically a test to ensure that you added the correct directory to path and the executable of the name novolign was detected properly.

The first line of every python file specifies which python to use

#!/usr/bin/python

is pretty typical.

[ashNZ]

OK... cheers first problem solved. I am now getting through the first few steps but am running into problems when the program is trying to find novoalign. I don't understand where to put that 'which novoalign' code that you told me.