issues with the error while loading shared libraries: libhts.so.1(already set the LD_LIBRARY_PATH)

[mengysun]

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]

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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[mengysun]

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]

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

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[mengysun]

​
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

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#10 (comment)

[zhqingit]

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

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#10 (comment)

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[mengysun]

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

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[zhqingit]

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

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#10 (comment)

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[mengysun]

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

[zhqingit]

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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[mengysun]

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

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