Have any of you tried the data of LSC paper?

[dis]

Have any of you tried the data of LSC paper?

I've downloaded brain data from http://www.stanford.edu/~kinfai/huma...m_PacBioLR.zip, and Illumina brain data from Human Body Map 2.0 GSE30611, and tried to reproduce the same result but I've got errors.

I wanted to make sure that I run LSC properly before I apply LSC to my data.
So, Here is my setting. LSC-0.2.2 with novoalign 2.07.10
I run example code from LSC website, successful, so I think all system setting should be good to go. I'm sure SR/LR dir and output, temp dir are correct. I failed in the middle of running

Traceback (most recent call last):
  File "/my/path/LSC_0.2.2/bin/writetmp.py", line 92, in <module>
    LR_SR_mapping_file = open(LR_SR_mapping_filename_ext,'r')   
IOError: [Errno 2] No such file or directory: 'temp_brain/LR_SR.map.aa'
0:29:42.983824
rm: cannot remove `temp_brain/LR_SR.map.aa': No such file or directory
rm: cannot remove `temp_brain/LR_SR.map.ab': No such file or directory
rm: cannot remove `temp_brain/LR_SR.map.ac': No such file or directory
rm: cannot remove `temp_brain/LR_SR.map.ad': No such file or directory
rm: cannot remove `temp_brain/LR_SR.map.ae': No such file or directory

[Richard Finney]

Use Google/duckduck/bing whatever on "errno 2"
Example : http://www.daemon-systems.org/man/errno.2.html

Errno 2 is file does not exist.

You might want to create temp_brain/ directory if it needs a place to create and write temp files otherwise you must figure out why the file named "temp_brain/LR_SR.map.aa" does not exist (perhaps you did not download some needed data in that directory). Try reading around line 92 in your python source file.

[dis]

Thank you, Richard
The folder exists, but not file. I'm examining python code now. Any other clue?

[winsettz]

What's the run number you are using for your Illumina data? The notes suggest input files as ".fa", which makes me think they are fasta without qual vs fastq.

I'm wondering if I can error-correct some Sanger data I have lying around, though at low coverage it may not be worth attempting.

[dis]

Thank you, winsettz. I agree with you.it's not worth to run if coverage is high enough.

The fasta that I ran is only bases not quals, so it fits LSC's specification.
I figured out the reason myself, it turns out LSC use many unix command and print its output to stdout as well as its log message. I tried to keep log message, that's why the program didn't work. I want them to fix this soon, hopefully.

[winsettz]

Thank you, winsettz. I agree with you.it's not worth to run if coverage is high enough.

The fasta that I ran is only bases not quals, so it fits LSC's specification.
I figured out the reason myself, it turns out LSC use many unix command and print its output to stdout as well as its log message. I tried to keep log message, that's why the program didn't work. I want them to fix this soon, hopefully.

I have an interesting issue where it's trying to execute

sh: /uniqseq2fasta.py: No such file or directory"

"/uniqseq2fasta.py", whereas it's intended to do "./uniqseq2fasta.py". I'm pretty sure something in runLSC.py is set up improperly. I wonder if I'm the only person with this issue.

Edit 2: Probably because I haven't set bin_path properly. Testing...

[dis]

Hi, winsettz

Have you ever moved the file uniqseq2fasta.py or runLSC.py?
So, it seems like runLSC is in the current directory ./ but uniqseq2fasta.py is not in ./
All .py of LSC should be in the same directory. That's how they set up bin_path.
I hope it'll help.

[LSC]

I have an interesting issue where it's trying to execute



"/uniqseq2fasta.py", whereas it's intended to do "./uniqseq2fasta.py". I'm pretty sure something in runLSC.py is set up improperly. I wonder if I'm the only person with this issue.

Edit 2: Probably because I haven't set bin_path properly. Testing...

Sorry for the late reply, folks~ I am just sort of busy on another big project currently. I just fixed this bin_path problem in LSC 0.2.3. Please try them and let me know if it works or not.

[LSC]

Could you please email your run.cfg and everything in the temp folder
("ls -ltr") to [email protected]?

Thank you, winsettz. I agree with you.it's not worth to run if coverage is high enough.

The fasta that I ran is only bases not quals, so it fits LSC's specification.
I figured out the reason myself, it turns out LSC use many unix command and print its output to stdout as well as its log message. I tried to keep log message, that's why the program didn't work. I want them to fix this soon, hopefully.