[winsettz]

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?

[ashNZ]

yep, got it. Where do I add that code?

[winsettz]

If you're running it interactively, then you would type out the command before running the python code.

[ashNZ]

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?

[winsettz]

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

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

[ashNZ]

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?

[winsettz]

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.

[ashNZ]

I tried various.... turns out it was a compatibility issue. All running fine now! Thanks a heap for all your help!

[winsettz]

Having lots of fun with the convertNAV.py

===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).

[sparks]

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

[MichalW]

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

[skycreative]

Hi, I think there is a bug in new version LSC2.0 deal with input files. As I tested, if input Long reads in fastq format will return error, while if input is fasta format will be OK.