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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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issues with the error while loading shared libraries: libhts.so.1(already set the LD_LIBRARY_PATH) #10

Open mengysun opened 8 years ago

mengysun commented 8 years ago

Hi Dr Zhang, I am trying to use the giremi program, but get the following error: "error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory". I have already set the LD_LIBRARY_PATH in the .bashrc file: LD_LIBRARY_PATH=/usr/local/lib/ But it doesn't work. How could I solve this issue? Best, Mengyi

zhqingit commented 8 years ago

Hi Mengyi,

It looks your hts library is not appropriately installed. Please make sure the libhts.so.1 can be found in /usr/local/lib.

Best, Qing

2016-03-23 9:23 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I am trying to use the giremi program, but get the following error: "error while loading shared libraries: libhts.so.1: cannot open shared object file: No such file or directory". I have already set the LD_LIBRARY_PATH in the .bashrc file: LD_LIBRARY_PATH=/usr/local/lib/ But it doesn't work. How could I solve this issue? Best, Mengyi

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10

mengysun commented 8 years ago

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

zhqingit commented 8 years ago

Hi Mengyi,

Can you send me the output file?

Best, Qing

2016-03-25 7:29 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201311601

mengysun commented 8 years ago

​ output https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VMWg3Nms5ZUx5OEE/view?usp=drive_web ​Hi Dr Zhang, Attached file is the output. Thank you! Best, Mengyi

On Fri, Mar 25, 2016 at 10:28 PM, zhqingit notifications@github.com wrote:

Hi Mengyi,

Can you send me the output file?

Best, Qing

2016-03-25 7:29 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201311601

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201678432

zhqingit commented 8 years ago

Hi Mengyi,

It looks the chromosome name in your fasta file is not consistent with that in your SNV list file. Could you send me your SNV lsit file and piece of the fasta file?

Best, Qing

2016-03-25 19:52 GMT-07:00 mengysun notifications@github.com:

​ output < https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VMWg3Nms5ZUx5OEE/view?usp=drive_web

​Hi Dr Zhang, Attached file is the output. Thank you! Best, Mengyi

On Fri, Mar 25, 2016 at 10:28 PM, zhqingit notifications@github.com wrote:

Hi Mengyi,

Can you send me the output file?

Best, Qing

2016-03-25 7:29 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201311601

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201678432

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201689971

mengysun commented 8 years ago

Hi Dr Zhang, Attached link is the snplist and the partial genome fasta. Best, Mengyi​ partial_fasta https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VQ2hFSkpQVzZOZHc/view?usp=drive_web ​​ dbsnplistNointergenic https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VSGZZQVZqVXEzQVk/view?usp=drive_web ​

On Tue, Mar 29, 2016 at 12:05 AM, zhqingit notifications@github.com wrote:

Hi Mengyi,

It looks the chromosome name in your fasta file is not consistent with that in your SNV list file. Could you send me your SNV lsit file and piece of the fasta file?

Best, Qing

2016-03-25 19:52 GMT-07:00 mengysun notifications@github.com:

​ output <

https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VMWg3Nms5ZUx5OEE/view?usp=drive_web

​Hi Dr Zhang, Attached file is the output. Thank you! Best, Mengyi

On Fri, Mar 25, 2016 at 10:28 PM, zhqingit notifications@github.com wrote:

Hi Mengyi,

Can you send me the output file?

Best, Qing

2016-03-25 7:29 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub <https://github.com/zhqingit/giremi/issues/10#issuecomment-201311601

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201678432

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201689971

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-202700684

zhqingit commented 8 years ago

Hi Mengyi,

Can you try to use your samtools to call some sites to see if the 'N' is got?

Best, Qing

2016-03-29 6:20 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, Attached link is the snplist and the partial genome fasta. Best, Mengyi​ partial_fasta < https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VQ2hFSkpQVzZOZHc/view?usp=drive_web

​​ dbsnplistNointergenic < https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VSGZZQVZqVXEzQVk/view?usp=drive_web

​

On Tue, Mar 29, 2016 at 12:05 AM, zhqingit notifications@github.com wrote:

Hi Mengyi,

It looks the chromosome name in your fasta file is not consistent with that in your SNV list file. Could you send me your SNV lsit file and piece of the fasta file?

Best, Qing

2016-03-25 19:52 GMT-07:00 mengysun notifications@github.com:

​ output <

https://drive.google.com/a/umich.edu/file/d/0B7AvjYHRyG2VMWg3Nms5ZUx5OEE/view?usp=drive_web

​Hi Dr Zhang, Attached file is the output. Thank you! Best, Mengyi

On Fri, Mar 25, 2016 at 10:28 PM, zhqingit notifications@github.com wrote:

Hi Mengyi,

Can you send me the output file?

Best, Qing

2016-03-25 7:29 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, I have already done that but it doesn't work. But I get it run on another computer anyway. On the other hand, I also faced the problem that the ifRNAE column is not generated. I check the scaffold names in the list and the reference fa file, it matches each other. So how could I solve this question? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub < https://github.com/zhqingit/giremi/issues/10#issuecomment-201311601

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub <https://github.com/zhqingit/giremi/issues/10#issuecomment-201678432

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-201689971

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-202700684

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-202890604

mengysun commented 8 years ago

Hi Dr Zhang, What do you mean by "if the 'N' is got"? Best, Mengyi

zhqingit commented 8 years ago

Hi Mengyi,

In your output file, all the nucleotides called from your fasta file are 'N'. So I guess there are some problems in your fasta file. You can use "samtools" to call several sites to see if the nucleotide is 'N' or not.

Best, Qing

2016-03-31 8:27 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, What do you mean by "if the 'N' is got"? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-203986344

mengysun commented 8 years ago

Thanks--sorry for the really late response. I would try it later. Best, Mengyi

On Thu, Mar 31, 2016 at 1:59 PM, zhqingit notifications@github.com wrote:

Hi Mengyi,

In your output file, all the nucleotides called from your fasta file are 'N'. So I guess there are some problems in your fasta file. You can use "samtools" to call several sites to see if the nucleotide is 'N' or not.

Best, Qing

2016-03-31 8:27 GMT-07:00 mengysun notifications@github.com:

Hi Dr Zhang, What do you mean by "if the 'N' is got"? Best, Mengyi

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-203986344

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/10#issuecomment-204055335