Plasmodium falciparum liftover
Vinay R S
I am not getting the .psl output or chain out puts.
Till chromosome sequence size is printing along with joblist but i am not getting any out put.
Could someone help me with this
Thanks in advance.
Regards
Vinay R S
Steve Heitner
Hello, Vinay.
I assume you are following the instructions at http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction. I have a few questions for you regarding this:
1. Do you have the additional kent source programs required by these scripts? (twoBitInfo, twoBitToFa, partitionSequence.pl, gensub2, blat, calc, axtChain)
2. Do you also have the companion script BlatJob.csh?
3. How did you obtain your query.2bit and target.2bit files?
4. Are there any error messages that might provide us additional help in diagnosing the problem?
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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Steve Heitner
Hello, Vinay.
I noticed in your output from SameSpeciesBlatSetup.sh, it shows:
./SameSpeciesBlatSetup.sh: line 98: blat: command not found
This is most certainly a major problem. The script calls blat along with all of the other additional kent source programs I listed previously. If you do indeed have these installed, you need to make sure their locations are specified in your PATH statement.
When you are in the directory you are running the script from, verify that the script will be able to successfully call blat by trying to run blat manually. If you cannot run blat manually from the command line, the script will likewise not be able to run blat and it will not succeed.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
From: Vinay R S [mailto:vina...@leucinerichbio.com]
Sent: Thursday, May 21, 2015 10:35 PM
To: st...@soe.ucsc.edu
Subject: Re: [genome] Plasmodium falciparum liftover
Hi Steve,
Yes i am following the instructions at http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction.
1. Yes i have all the additional kent source programs required as above mentioned.
2. I also have the companion script Blatjob.csh.
3. I have converted the 2005 fasta sequence as query.2bit and 2015 fasta sequence as target.2bit using faToTwoBit tool.
in both query and target sequence contains all 14 chromosome fasta sequence
4. when i run ./SameSpeciesBlatSetup.sh i get the following output in terminal
lrb@lrb-desktop:~/Desktop/testing/malaria/liftover$ ./SameSpeciesBlatSetup.sh
Unmatched parenthesis
./SameSpeciesBlatSetup.sh: line 98: blat: command not found
lrb@lrb-desktop:~/Desktop/testing/malaria/liftover$ ./SameSpeciesBlatSetup.sh
Unmatched parenthesis
Loading /home/lrb/Desktop/testing/malaria/liftover/twobit/tar.2bit
Counting /home/lrb/Desktop/testing/malaria/liftover/twobit/tar.2bit
Writing 11.ooc
Wrote 3129 overused 11-mers to 11.ooc
Done making 11.ooc
5. After running this script inside run.blat/psl folder there will be all 14 folders with part000.lst to part013.lst but there wont be any .psl files inside these folders which supposed to be output chain files i guess.
6. When i run SameSpeciesChainNet.sh i get this following error.
lrb@lrb-desktop:~/Desktop/testing/malaria/liftover$ ./SameSpeciesChainNet.sh
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)
I have enclosed all the scripts with the changes as per my local variables.
Kindly help me with this issue.
Thanks and Regards
Vinay R S