SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Beg for latest version of SOAPdenovo correction tool before assembly zhongj Illumina/Solexa 2 02-26-2012 06:56 PM
PerM is an ultra-fast and sensitive SOLiD reads mapping tool KevinLam Bioinformatics 7 06-18-2010 04:03 AM
Fast and accurate long read alignment with Burrows-Wheeler transform. nilshomer Literature Watch 1 01-28-2010 10:38 PM
BFAST and read error correction (with SAET or similar tool) javijevi Bioinformatics 4 01-27-2010 01:46 PM

Reply
 
Thread Tools
Old 05-21-2013, 05:38 AM   #41
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

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?
ashNZ is offline   Reply With Quote
Old 05-21-2013, 12:26 PM   #42
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

Quote:
Originally Posted by ashNZ View Post
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.

Code:
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.
winsettz is offline   Reply With Quote
Old 05-22-2013, 05:34 AM   #43
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

Quote:
Originally Posted by winsettz View Post
Don't need to.

Code:
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
ashNZ is offline   Reply With Quote
Old 05-22-2013, 06:23 AM   #44
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

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

Code:
#!/usr/bin/python
is pretty typical.
winsettz is offline   Reply With Quote
Old 05-22-2013, 12:16 PM   #45
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

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.
ashNZ is offline   Reply With Quote
Old 05-22-2013, 12:17 PM   #46
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

which novoalign is just a test to see if you set up the path correctly.

All you really need is PATH=/directory...:$PATH

Do you have a copy of novoalign?
winsettz is offline   Reply With Quote
Old 05-22-2013, 12:19 PM   #47
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

yep, got it. Where do I add that code?
ashNZ is offline   Reply With Quote
Old 05-22-2013, 12:20 PM   #48
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

If you're running it interactively, then you would type out the command before running the python code.
winsettz is offline   Reply With Quote
Old 05-22-2013, 12:26 PM   #49
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

When I run the program, it goes through the first few steps all good and then when it gets to these steps I have errors with not finding novoalign:

===novoindex pseudochr:===
sh: 1: novoindex: not found
0:00:43.058524
===novoalign SR.aa.cps:===
sh: 1: novoalign: not found
sh: 1: sh: 1: novoalign: not found
novoalign: not found
sh: 1: novoalign: not found
0:00:43.062321

I tried using your code by typing in the terminal, just before I executed the script:

PATH=/home/ash/Bioinformatics/novocraft/novoalign:$PATH

Is that what you were meaning or am I making a mistake here?
ashNZ is offline   Reply With Quote
Old 05-22-2013, 12:28 PM   #50
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

My guess is that you are setting the path to the executable, instead of the directory the executable is in. In that case, it should be
Code:
PATH=/home/ash/Bioinformatics/novocraft:$PATH
winsettz is offline   Reply With Quote
Old 05-22-2013, 12:35 PM   #51
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

Yep, I was most definitely doing that! Cheers for the help.... now when it gets to the novoindex bit its saying:

===novoindex pseudochr:===
/home/ash/Bioinformatics/novocraft/novoindex: 1: /home/ash/Bioinformatics/novocraft/novoindex: Syntax error: "(" unexpected
0:00:44.197463

then there are also a whole bunch of errors relating to novoalign:

===novoalign SR.aa.cps:===
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: /home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: ELF: not foundELF: not found

/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: /home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
ELF: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign:
ELF: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: 0/ȳ: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: 0/ȳ: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: 0Q�tdR�tdX: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: 0Q�tdR�tdX: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: X: not found
/home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: /home/ash/Bioinformatics/novocraft/novoalign: 1: /home/ash/Bioinformatics/novocraft/novoalign: �$�$GNUSuSESuSE: not found�$�$GNUSuSESuSE: not found

it then tries again for novoalign: 2 and 3......

any ideas what the issue here could be? Am I lacking some other software I need for the OS to be able to execute novoalign?
ashNZ is offline   Reply With Quote
Old 05-22-2013, 01:32 PM   #52
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

I've not seen that issue. Which version of novolign are you using? i've tested it on a centos 6.4 system using novoalign 2.08.03.

It's possible novoalign isn't compatible with your operating system. The release notes suggest that it should work relatively out-of-the-box.

Last edited by winsettz; 05-22-2013 at 02:53 PM.
winsettz is offline   Reply With Quote
Old 05-24-2013, 05:23 AM   #53
ashNZ
Member
 
Location: Minas Gerais, Brazil

Join Date: May 2013
Posts: 11
Default

I tried various.... turns out it was a compatibility issue. All running fine now! Thanks a heap for all your help!
ashNZ is offline   Reply With Quote
Old 05-24-2013, 06:49 AM   #54
winsettz
Member
 
Location: US

Join Date: Sep 2012
Posts: 91
Default

Having lots of fun with the convertNAV.py

Code:
===convertNAV SR.aa.cps.nav:===
Traceback (most recent call last):
  File "/data4/experpath/vasm/vasm/NextGen/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
Traceback (most recent call last):
  File "/data4/experpath/vasm/vasm/NextGen/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
Traceback (most recent call last):
  File "/data4/experpath/vasm/vasm/NextGen/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
  File "/data4/experpath/vasm/vasm/NextGen/setoc/Programs/LSC/LSC_023/convertNAV.py", line 49, in <module>
    start_pt = int(line_list[3])
    start_pt = int(line_list[3])
IndexError: list index out of range
IndexError: list index out of range
        start_pt = int(line_list[3])
start_pt = int(line_list[3])
IndexErrorIndexError: : list index out of rangelist index out of range
Going to bite the bullet and start poking into the source. It seems to happen on on exceedingly large LR files, and not smaller ones (such as subsets of data).
winsettz is offline   Reply With Quote
Old 12-02-2013, 05:26 AM   #55
sparks
Senior Member
 
Location: Kuala Lumpur, Malaysia

Join Date: Mar 2008
Posts: 126
Default

Hi,

If you are using Novoalign with LSC you need to use -r Exhaustive not -r All.

From my tests good options are..

novoalign -c1 -r Ex 1000 -t 250 -F FA -g 0 -x 30 -o sam

This will give much better results than BWA and reduce total run time.

I'm making some mod's to novoalign that should help even further. Expect some changes in V3.03

Colin
sparks is offline   Reply With Quote
Old 02-14-2014, 06:34 AM   #56
MichalW
Junior Member
 
Location: Poland

Join Date: Feb 2014
Posts: 1
Default RazerS3

Hi,

I'm trying to use RazerS3 in LSC but I've got problems with starting it. I'm not sure if I congigured run.cfg correctly or is it something else ex. software.

Here is log:
=== Welcome to LSC 1.alpha ===
[python_path , /usr/bin/python]
[mode , 0]
[LR_pathfilename , /home/michal/Documents/Genome/PacBio/correction/LSC_1_alpha/data/m121204_060938_42158_c100418292550000001523037201151324_s1_p0.filtered_subreads.fq]
[LR_filetype , fq]
[SR_pathfilename , /home/michal/Documents/Genome/PacBio/correction/LSC_1_alpha/data/HI_0635_008_Index_12_A_R1.fq]
[SR_filetype , fq]
[I_nonredundant , N]
[SCD , 20]
[Nthread1 , 18]
[Nthread2 , 18]
[sort_max_mem , 8G]
[temp_foldername , temp]
[output_foldername , output]
[I_RemoveBothTails , Y]
[MinNumberofNonN , 39]
[MaxN , 1]
[clean_up , 1]
[aligner , razers3]
[novoalign_options , -r All -F FA -n 300 -o sam -o]
[bwa_options , -n 0.08 -o 20 -e 3 -d 0 -i 0 -M 1 -O 0 -E 1 -N]
[bowtie2_options , --end-to-end -a -f -L 15 --mp 1,1 --np 1 --rdg 0,1 --rfg 0,1 --score-min L,0,-0.08 --no-unal]
[razers3_options , -i 92 -mr 0 -of sam]
=== sort and uniq SR data ===
0:22:17.325225
===split SR:===
0:22:36.830348
===compress SR.??:===
0:03:44.589961
finsish genome
0:03:53.335585
finsish genome
0:04:02.438411
finsish genome
0:04:04.346571
finsish genome
0:04:05.632314
finsish genome
0:04:05.908455
finsish genome
0:04:13.855829
finsish genome
0:04:14.051202
finsish genome
0:04:16.863315
finsish genome
0:04:18.913044
finsish genome
0:04:19.578576
finsish genome
0:04:22.985824
finsish genome
0:04:28.191675
finsish genome
0:04:29.413262
finsish genome
0:04:30.487522
finsish genome
0:04:32.444715
finsish genome
0:04:33.872014
finsish genome
0:04:38.683421
finsish genome
0:27:15.556423
===RemoveBothTails in LR:===
0:27:17.408112
/usr/bin/python ./FASTA2fa.py temp/Notwotails_m121204_060938_42158_c100418292550000001523037201151324_s1_p0.filtered_subreads.fq temp/LR.fa
rm temp/Notwotails_m121204_060938_42158_c100418292550000001523037201151324_s1_p0.filtered_subreads.fq
0:27:17.910498
===compress LR:===
/usr/bin/python ./compress.py -MinNonN=39 -MaxN=10000 fa temp/LR.fa temp/LR.fa.
0:00:23.191412
finsish genome
rm temp/LR.fa
0:27:45.242358
===razers3 SR.??.cps:===
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...r
azers3: invalid combination of arguments -- -of

Exiting ...
razers3: invalid combination of arguments -- -of

Exiting ...
0:27:45.276017
===samParser SR.??.cps.nav:===
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ab.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.aq.cps.sam'
Traceback (most recent call last):
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
sam_file = open(sam_filename, 'r')
IOErrorIOError: [Errno 2] No such file or directory: 'temp/SR.fa.af.cps.sam':
[Errno 2] No such file or directory: 'temp/SR.fa.ak.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ac.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ae.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ap.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.am.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.aa.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.aj.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ad.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ai.cps.sam'
Traceback (most recent call last):
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
sam_file = open(sam_filename, 'r')
IOErrorIOError: : [Errno 2] No such file or directory: 'temp/SR.fa.al.cps.sam'
[Errno 2] No such file or directory: 'temp/SR.fa.ao.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ag.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ah.cps.sam'
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
Traceback (most recent call last):
File "./samParser.py", line 72, in <module>
sam_file = open(sam_filename, 'r')
IOError: IOError: [Errno 2] No such file or directory: 'temp/SR.fa.ar.cps.sam'
[Errno 2] No such file or directory: 'temp/SR.fa.an.cps.sam'
0:27:46.039458
===cat SR.??.cps:===
0:30:06.209277
===cat SR.??.idx:===
0:32:31.989657
===cat SR.??.cps.sam :===
cat: temp/SR.fa.aa.cps.sam: No such file or directory
cat: temp/SR.fa.ab.cps.sam: No such file or directory
cat: temp/SR.fa.ac.cps.sam: No such file or directory
cat: temp/SR.fa.ad.cps.sam: No such file or directory
cat: temp/SR.fa.ae.cps.sam: No such file or directory
cat: temp/SR.fa.af.cps.sam: No such file or directory
cat: temp/SR.fa.ag.cps.sam: No such file or directory
cat: temp/SR.fa.ah.cps.sam: No such file or directory
cat: temp/SR.fa.ai.cps.sam: No such file or directory
cat: temp/SR.fa.aj.cps.sam: No such file or directory
cat: temp/SR.fa.ak.cps.sam: No such file or directory
cat: temp/SR.fa.al.cps.sam: No such file or directory
cat: temp/SR.fa.am.cps.sam: No such file or directory
cat: temp/SR.fa.an.cps.sam: No such file or directory
cat: temp/SR.fa.ao.cps.sam: No such file or directory
cat: temp/SR.fa.ap.cps.sam: No such file or directory
cat: temp/SR.fa.aq.cps.sam: No such file or directory
cat: temp/SR.fa.ar.cps.sam: No such file or directory
0:32:31.998292
===cat SR.??.cps.nav :===
cat: temp/SR.fa.aa.cps.nav: No such file or directory
cat: temp/SR.fa.ab.cps.nav: No such file or directory
cat: temp/SR.fa.ac.cps.nav: No such file or directory
cat: temp/SR.fa.ad.cps.nav: No such file or directory
cat: temp/SR.fa.ae.cps.nav: No such file or directory
cat: temp/SR.fa.af.cps.nav: No such file or directory
cat: temp/SR.fa.ag.cps.nav: No such file or directory
cat: temp/SR.fa.ah.cps.nav: No such file or directory
cat: temp/SR.fa.ai.cps.nav: No such file or directory
cat: temp/SR.fa.aj.cps.nav: No such file or directory
cat: temp/SR.fa.ak.cps.nav: No such file or directory
cat: temp/SR.fa.al.cps.nav: No such file or directory
cat: temp/SR.fa.am.cps.nav: No such file or directory
cat: temp/SR.fa.an.cps.nav: No such file or directory
cat: temp/SR.fa.ao.cps.nav: No such file or directory
cat: temp/SR.fa.ap.cps.nav: No such file or directory
cat: temp/SR.fa.aq.cps.nav: No such file or directory
cat: temp/SR.fa.ar.cps.nav: No such file or directory
0:32:32.004572
rm: cannot remove `temp/SR.fa.aa.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.aa.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.ab.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.ab.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.ac.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.ac.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.ad.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.ad.cps.sam': No such file or directory
rm: rm: cannot remove `temp/SR.fa.ae.cps.nav'cannot remove `temp/SR.fa.ae.cps.sam': No such file or directory: No such file or directory

rm: rm: cannot remove `temp/SR.fa.af.cps.sam'cannot remove `temp/SR.fa.af.cps.nav': No such file or directory
: No such file or directory
rm: cannot remove `temp/SR.fa.ag.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.ag.cps.sam': No such file or directory
rm: rm: cannot remove `temp/SR.fa.ah.cps.nav'cannot remove `temp/SR.fa.ah.cps.sam': No such file or directory
: No such file or directory
rm: cannot remove `temp/SR.fa.ai.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.ai.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.aj.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.aj.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.ak.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.ak.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.al.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.al.cps.sam': No such file or directory
rm: rm: cannot remove `temp/SR.fa.am.cps.nav'cannot remove `temp/SR.fa.am.cps.sam': No such file or directory
rm: cannot remove `temp/SR.fa.an.cps.nav': No such file or directory
rm: cannot remove `temp/SR.fa.an.cps.sam': No such file or directory
: No such file or directory
rm: rm: cannot remove `temp/SR.fa.ao.cps.sam'cannot remove `temp/SR.fa.ao.cps.nav': No such file or directory: No such file or directory

rm: rm: cannot remove `temp/SR.fa.ap.cps.sam': No such file or directorycannot remove `temp/SR.fa.ap.cps.nav': No such file or directory

rm: cannot remove `temp/SR.fa.aq.cps.nav'rm: cannot remove `temp/SR.fa.aq.cps.sam': No such file or directory
: No such file or directory
rm: rm: cannot remove `temp/SR.fa.ar.cps.nav'cannot remove `temp/SR.fa.ar.cps.sam': No such file or directory: No such file or directory

===genLR_SRmapping SR.??.cps.nav:===
Error: No short reads was aligned to long read. LSC could not correct any long read sequence.
0:32:33.149550
===split LR_SR.map:===
Traceback (most recent call last):
File "runLSC.py", line 535, in <module>
LR_SR_map_NR = int(commands.getstatusoutput('wc -l ' + temp_foldername +"LR_SR.map")[1].split()[0])
ValueError: invalid literal for int() with base 10: 'wc:'

Really looking forward for the solution or some tips
MichalW is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO