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