Comments (14)
amnona
commented on June 29, 2024
Hi Bishnu,
deblur_working_dir is a temporary directory produced by deblur during the
processing.
If you see this directory but not the reference-hit.biom etc. it means one
of the two:
1. deblur is still running
2. deblur failed during the processing.
Did deblur output some error message?
Also, you can look at the deblur.log file to see exactly where the problem
occurs.
I would recommend deleting deblur.log (since new output is appended to the
log file rather than rewriting it) and then rerunning deblur with more
verbose log reporting. i.e.
deblur (ALL YOUR PARAMETERS) --log-level 1
Can you copy the exact command you used for running deblur, and attach the
deblur.log file after rerunning?
Cheers
Amnon
…On Wed, Jul 11, 2018 at 6:42 PM Bishnu Adhikari ***@***.***> wrote:
I was running deblur workflow using seqs.fna, output from
split_libraries_fastq.py as demonstrated in the example, however, I was
getting different outputs than those mentioned in the example. I am getting
deblur_working_dir, deblur.log and split as outputs instead of getting
reference-hit.seqs.fa, reference-non-hit.biom, reference-non-hit.biom,
reference-non-hit.seqs.fa, all.biom, and all.seqs.fa as mentioned in the
example. I used the deblur workflow previously once but was getting the
exact outputs. I am wondering whether, the workflow has changed or
something wrong, and I didn't see any changes in the github example usage.
I didn't have any ideas how to use the information in current directories
for futher downstream analysis if the output is correct. I would really
appreciate your suggestions and feebacks on this issue.
Thank you
Best Regards
Bishnu Adhikari
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bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Thank you very much for the quick reply. I have re-ran as you suggested and
got the following error message. The exact code I have entered is also
shown below.
(deblurenv) bxa015@js-16-234:~/Kemin-BA/joined_pairend/processed_seqs/split_kemin$
deblur workflow --seqs-fp seqs.fna --output-dir output -t 400
Traceback (most recent call last):
File "/home/bxa015/miniconda3/envs/deblurenv/bin/deblur", line 684, in
<module>
deblur_cmds()
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py",
line 722, in __call__
return self.main(*args, **kwargs)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py",
line 697, in main
rv = self.invoke(ctx)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py",
line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py",
line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/click/core.py",
line 535, in invoke
return callback(*args, **kwargs)
File "/home/bxa015/miniconda3/envs/deblurenv/bin/deblur", line 655, in
workflow
outputfasta_fp=outputfasta_fp, minreads=min_reads)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/deblur/workflow.py",
line 705, in create_otu_table
obs = scipy.sparse.dok_matrix((1E9, len(deblurred_list)),
dtype=np.double)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/scipy/sparse/dok.py",
line 88, in __init__
self._shape = check_shape((M, N))
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/scipy/sparse/sputils.py",
line 281, in check_shape
new_shape = tuple(operator.index(arg) for arg in args)
File
"/home/bxa015/miniconda3/envs/deblurenv/lib/python3.5/site-packages/scipy/sparse/sputils.py",
line 281, in <genexpr>
new_shape = tuple(operator.index(arg) for arg in args)
TypeError: 'float' object cannot be interpreted as an integer
(deblurenv) bxa015@js-16-234
:~/Kemin-BA/joined_pairend/processed_seqs/split_kemin$
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
…On Wed, Jul 11, 2018 at 12:18 PM, amnona ***@***.***> wrote:
Hi Bishnu,
deblur_working_dir is a temporary directory produced by deblur during the
processing.
If you see this directory but not the reference-hit.biom etc. it means one
of the two:
1. deblur is still running
2. deblur failed during the processing.
Did deblur output some error message?
Also, you can look at the deblur.log file to see exactly where the problem
occurs.
I would recommend deleting deblur.log (since new output is appended to the
log file rather than rewriting it) and then rerunning deblur with more
verbose log reporting. i.e.
deblur (ALL YOUR PARAMETERS) --log-level 1
Can you copy the exact command you used for running deblur, and attach the
deblur.log file after rerunning?
Cheers
Amnon
On Wed, Jul 11, 2018 at 6:42 PM Bishnu Adhikari ***@***.***>
wrote:
> I was running deblur workflow using seqs.fna, output from
> split_libraries_fastq.py as demonstrated in the example, however, I was
> getting different outputs than those mentioned in the example. I am
getting
> deblur_working_dir, deblur.log and split as outputs instead of getting
> reference-hit.seqs.fa, reference-non-hit.biom, reference-non-hit.biom,
> reference-non-hit.seqs.fa, all.biom, and all.seqs.fa as mentioned in the
> example. I used the deblur workflow previously once but was getting the
> exact outputs. I am wondering whether, the workflow has changed or
> something wrong, and I didn't see any changes in the github example
usage.
> I didn't have any ideas how to use the information in current directories
> for futher downstream analysis if the output is correct. I would really
> appreciate your suggestions and feebacks on this issue.
>
> Thank you
>
> Best Regards
> Bishnu Adhikari
>
> —
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bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Please find the deblur log ran a/c to your suggestions which also got the same error message as above when I gave following command.
(deblurenv) bxa015@js-16-234:~$ deblur workflow --seqs-fp seqs.fna --output-dir output -t 400 --log-level 1
deblur.log
Thank you
Regards
Bishnu Adhikari
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amnona
commented on June 29, 2024
Hi Bishnu,
This seems to be a bug in the deblur code due to a change in how python
treats 1E9 (float rather than int) in new python versions.
We're working on a fix. Will update once it is ready.
Thanks for the report
Amnon
…On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari ***@***.***> wrote:
Dear Amnon,
Please find the deblur log ran a/c to your suggestions which also got the
same error message as above when I gave following command.
(deblurenv) ***@***.***:~$ deblur workflow --seqs-fp seqs.fna
--output-dir output -t 400 --log-level 1
deblur.log <https://github.com/biocore/deblur/files/2186150/deblur.log>
Thank you
Regards
Bishnu Adhikari
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bishnuadhikari
commented on June 29, 2024
Dear Amnona,
Thank you very much for the information. Please let me know once it is
fixed. I hope it will be fixed soon.
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
…On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***> wrote:
Hi Bishnu,
This seems to be a bug in the deblur code due to a change in how python
treats 1E9 (float rather than int) in new python versions.
We're working on a fix. Will update once it is ready.
Thanks for the report
Amnon
On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari ***@***.***
>
wrote:
> Dear Amnon,
>
> Please find the deblur log ran a/c to your suggestions which also got the
> same error message as above when I gave following command.
> (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp seqs.fna
> --output-dir output -t 400 --log-level 1
>
> deblur.log <https://github.com/biocore/deblur/files/2186150/deblur.log>
> Thank you
> Regards
> Bishnu Adhikari
>
> —
> You are receiving this because you commented.
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> <#176 (comment)>,
or mute
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bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Good afternoon,
I am just checking whether bug in the deblur workflow is fixed or not. I
really appreciate you kind support and help.
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <[email protected]>
wrote:
… Dear Amnona,
Thank you very much for the information. Please let me know once it is
fixed. I hope it will be fixed soon.
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***> wrote:
> Hi Bishnu,
> This seems to be a bug in the deblur code due to a change in how python
> treats 1E9 (float rather than int) in new python versions.
> We're working on a fix. Will update once it is ready.
>
> Thanks for the report
> Amnon
>
> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> ***@***.***>
> wrote:
>
> > Dear Amnon,
> >
> > Please find the deblur log ran a/c to your suggestions which also got
> the
> > same error message as above when I gave following command.
> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp seqs.fna
> > --output-dir output -t 400 --log-level 1
> >
> > deblur.log <https://github.com/biocore/deblur/files/2186150/deblur.log>
> > Thank you
> > Regards
> > Bishnu Adhikari
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#176 (comment)>,
> or mute
> > the thread
> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
>
> > .
> >
>
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amnona
commented on June 29, 2024
Hi,
Should be ready in 24hrs. Will mail when merged and ready for install.
Thanks
Amnon
On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari <[email protected]>
wrote:
… Dear Amnon,
Good afternoon,
I am just checking whether bug in the deblur workflow is fixed or not. I
really appreciate you kind support and help.
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari ***@***.***>
wrote:
> Dear Amnona,
>
> Thank you very much for the information. Please let me know once it is
> fixed. I hope it will be fixed soon.
>
> Best Regards
> Bishnu Adhikari
> PhD Candidate
> University of Arkansas
> Poultry Science POSC O-220
> 1260 W. Maple
> Fayetteville, AR 72701
> 4798562305
>
> On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***>
wrote:
>
>> Hi Bishnu,
>> This seems to be a bug in the deblur code due to a change in how python
>> treats 1E9 (float rather than int) in new python versions.
>> We're working on a fix. Will update once it is ready.
>>
>> Thanks for the report
>> Amnon
>>
>> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
>> ***@***.***>
>> wrote:
>>
>> > Dear Amnon,
>> >
>> > Please find the deblur log ran a/c to your suggestions which also got
>> the
>> > same error message as above when I gave following command.
>> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp seqs.fna
>> > --output-dir output -t 400 --log-level 1
>> >
>> > deblur.log <
https://github.com/biocore/deblur/files/2186150/deblur.log>
>> > Thank you
>> > Regards
>> > Bishnu Adhikari
>> >
>> > —
>> > You are receiving this because you commented.
>> > Reply to this email directly, view it on GitHub
>> > <#176 (comment)
>,
>> or mute
>> > the thread
>> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
>> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
>>
>> > .
>> >
>>
>> —
>> You are receiving this because you authored the thread.
>> Reply to this email directly, view it on GitHub
>> <
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_biocore_deblur_issues_176-23issuecomment-2D405050225&d=DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=VdUecPkVFhn38jM8aYFL6Q&m=oiHL8g02sLNeLWfSJqxjDm1FYrD-VxNwSxsweOVZ0Bc&s=BbEVTy08p4jXHTT8MLTUH3hJkBu8I-Mnunz9XobiSW4&e=
>,
>> or mute the thread
>> <
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ARVbfi2xVtM1sgmPxd4PSAHUl-5FDkTO5xks5uGl7NgaJpZM4VLYwz&d=DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=VdUecPkVFhn38jM8aYFL6Q&m=oiHL8g02sLNeLWfSJqxjDm1FYrD-VxNwSxsweOVZ0Bc&s=5Zz03_B4lf08At2yh2n930p7xgnE5RAYXydCZFo9RZA&e=
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>> .
>>
>
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bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Thank you very much for the information. I am eagerly waiting to run it
again.
Appreciated.
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
…On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***> wrote:
Hi,
Should be ready in 24hrs. Will mail when merged and ready for install.
Thanks
Amnon
On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari ***@***.***>
wrote:
> Dear Amnon,
>
> Good afternoon,
>
> I am just checking whether bug in the deblur workflow is fixed or not. I
> really appreciate you kind support and help.
>
> Thank you
>
> Best Regards
> Bishnu Adhikari
> PhD Candidate
> University of Arkansas
> Poultry Science POSC O-220
> 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>>
Fayetteville, AR 72701
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
> 4798562305
>
> On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari ***@***.***>
> wrote:
>
> > Dear Amnona,
> >
> > Thank you very much for the information. Please let me know once it is
> > fixed. I hope it will be fixed soon.
> >
> > Best Regards
> > Bishnu Adhikari
> > PhD Candidate
> > University of Arkansas
> > Poultry Science POSC O-220
> > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>>
> Fayetteville, AR 72701
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
> > 4798562305
> >
> > On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***>
> wrote:
> >
> >> Hi Bishnu,
> >> This seems to be a bug in the deblur code due to a change in how
python
> >> treats 1E9 (float rather than int) in new python versions.
> >> We're working on a fix. Will update once it is ready.
> >>
> >> Thanks for the report
> >> Amnon
> >>
> >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> >> ***@***.***>
> >> wrote:
> >>
> >> > Dear Amnon,
> >> >
> >> > Please find the deblur log ran a/c to your suggestions which also
got
> >> the
> >> > same error message as above when I gave following command.
> >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp seqs.fna
> >> > --output-dir output -t 400 --log-level 1
> >> >
> >> > deblur.log <
> https://github.com/biocore/deblur/files/2186150/deblur.log>
> >> > Thank you
> >> > Regards
> >> > Bishnu Adhikari
> >> >
> >> > —
> >> > You are receiving this because you commented.
> >> > Reply to this email directly, view it on GitHub
> >> > <#176#
issuecomment-404305789
> >,
> >> or mute
> >> > the thread
> >> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
> >> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
> >>
> >> > .
> >> >
> >>
> >> —
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> >>
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from deblur.
amnona
commented on June 29, 2024
Hi Bishnu,
we have a new dev. version on github that should take care of this bug.
Can you try to install the github version as follows:
source activate deblurenv
conda uninstall deblur
pip install git+git://github.com/biocore/deblur
and then try to run deblur on your data?
Please let me know if it works now or if the bug is still occurring.
Thanks,
Amnon
On Thu, Jul 19, 2018 at 9:53 PM Bishnu Adhikari <[email protected]>
wrote:
… Dear Amnon,
Thank you very much for the information. I am eagerly waiting to run it
again.
Appreciated.
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***> wrote:
> Hi,
> Should be ready in 24hrs. Will mail when merged and ready for install.
>
> Thanks
> Amnon
>
> On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari ***@***.***>
>
> wrote:
>
> > Dear Amnon,
> >
> > Good afternoon,
> >
> > I am just checking whether bug in the deblur workflow is fixed or not.
I
> > really appreciate you kind support and help.
> >
> > Thank you
> >
> > Best Regards
> > Bishnu Adhikari
> > PhD Candidate
> > University of Arkansas
> > Poultry Science POSC O-220
> > 1260 W. Maple
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
>
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>>
> Fayetteville, AR 72701
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
> > 4798562305
> >
> > On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <
***@***.***>
> > wrote:
> >
> > > Dear Amnona,
> > >
> > > Thank you very much for the information. Please let me know once it
is
> > > fixed. I hope it will be fixed soon.
> > >
> > > Best Regards
> > > Bishnu Adhikari
> > > PhD Candidate
> > > University of Arkansas
> > > Poultry Science POSC O-220
> > > 1260 W. Maple
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
>
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>>
> > Fayetteville, AR 72701
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
> > > 4798562305
> > >
> > > On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***>
> > wrote:
> > >
> > >> Hi Bishnu,
> > >> This seems to be a bug in the deblur code due to a change in how
> python
> > >> treats 1E9 (float rather than int) in new python versions.
> > >> We're working on a fix. Will update once it is ready.
> > >>
> > >> Thanks for the report
> > >> Amnon
> > >>
> > >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> > >> ***@***.***>
> > >> wrote:
> > >>
> > >> > Dear Amnon,
> > >> >
> > >> > Please find the deblur log ran a/c to your suggestions which also
> got
> > >> the
> > >> > same error message as above when I gave following command.
> > >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp
seqs.fna
> > >> > --output-dir output -t 400 --log-level 1
> > >> >
> > >> > deblur.log <
> > https://github.com/biocore/deblur/files/2186150/deblur.log>
> > >> > Thank you
> > >> > Regards
> > >> > Bishnu Adhikari
> > >> >
> > >> > —
> > >> > You are receiving this because you commented.
> > >> > Reply to this email directly, view it on GitHub
> > >> > <#176#
> issuecomment-404305789
> > >,
> > >> or mute
> > >> > the thread
> > >> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
> > >> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
> > >>
> > >> > .
> > >> >
> > >>
> > >> —
> > >> You are receiving this because you authored the thread.
> > >> Reply to this email directly, view it on GitHub
> > >> <
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_biocore_deblur_issues_176-23issuecomment-2D405050225&d=
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> > >> or mute the thread
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> B4lf08At2yh2n930p7xgnE5RAYXydCZFo9RZA&e=
> > >
> > >> .
> > >>
> > >
> > >
> >
> > —
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from deblur.
bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Thank you very much for the information and support. Now, I got the results
and worked perfectly. I want to know your suggeston regarding trim length;
the median sequence length of the reads is 548 since each forward and
reverse reads were 300 bp and joined together. At this condition, what trim
length will be optimum based on your experience?
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
…On Sun, Jul 22, 2018 at 9:46 AM, amnona ***@***.***> wrote:
Hi Bishnu,
we have a new dev. version on github that should take care of this bug.
Can you try to install the github version as follows:
source activate deblurenv
conda uninstall deblur
pip install git+git://github.com/biocore/deblur
and then try to run deblur on your data?
Please let me know if it works now or if the bug is still occurring.
Thanks,
Amnon
On Thu, Jul 19, 2018 at 9:53 PM Bishnu Adhikari ***@***.***>
wrote:
> Dear Amnon,
>
>
> Thank you very much for the information. I am eagerly waiting to run it
> again.
>
> Appreciated.
>
> Best Regards
> Bishnu Adhikari
> PhD Candidate
> University of Arkansas
> Poultry Science POSC O-220
> 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>>
Fayetteville, AR 72701
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
> 4798562305
>
> On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***>
wrote:
>
> > Hi,
> > Should be ready in 24hrs. Will mail when merged and ready for install.
> >
> > Thanks
> > Amnon
> >
> > On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari <
***@***.***>
> >
> > wrote:
> >
> > > Dear Amnon,
> > >
> > > Good afternoon,
> > >
> > > I am just checking whether bug in the deblur workflow is fixed or
not.
> I
> > > really appreciate you kind support and help.
> > >
> > > Thank you
> > >
> > > Best Regards
> > > Bishnu Adhikari
> > > PhD Candidate
> > > University of Arkansas
> > > Poultry Science POSC O-220
> > > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> >
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >>
> > Fayetteville, AR 72701
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> > > 4798562305
> > >
> > > On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <
> ***@***.***>
> > > wrote:
> > >
> > > > Dear Amnona,
> > > >
> > > > Thank you very much for the information. Please let me know once it
> is
> > > > fixed. I hope it will be fixed soon.
> > > >
> > > > Best Regards
> > > > Bishnu Adhikari
> > > > PhD Candidate
> > > > University of Arkansas
> > > > Poultry Science POSC O-220
> > > > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> >
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >>
> > > Fayetteville, AR 72701
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> > > > 4798562305
> > > >
> > > > On Sat, Jul 14, 2018 at 4:12 PM, amnona ***@***.***>
> > > wrote:
> > > >
> > > >> Hi Bishnu,
> > > >> This seems to be a bug in the deblur code due to a change in how
> > python
> > > >> treats 1E9 (float rather than int) in new python versions.
> > > >> We're working on a fix. Will update once it is ready.
> > > >>
> > > >> Thanks for the report
> > > >> Amnon
> > > >>
> > > >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> > > >> ***@***.***>
> > > >> wrote:
> > > >>
> > > >> > Dear Amnon,
> > > >> >
> > > >> > Please find the deblur log ran a/c to your suggestions which
also
> > got
> > > >> the
> > > >> > same error message as above when I gave following command.
> > > >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp
> seqs.fna
> > > >> > --output-dir output -t 400 --log-level 1
> > > >> >
> > > >> > deblur.log <
> > > https://github.com/biocore/deblur/files/2186150/deblur.log>
> > > >> > Thank you
> > > >> > Regards
> > > >> > Bishnu Adhikari
> > > >> >
> > > >> > —
> > > >> > You are receiving this because you commented.
> > > >> > Reply to this email directly, view it on GitHub
> > > >> > <#176#
> > issuecomment-404305789
> > > >,
> > > >> or mute
> > > >> > the thread
> > > >> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
> > > >> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
> > > >>
> > > >> > .
> > > >> >
> > > >>
> > > >> —
> > > >> You are receiving this because you authored the thread.
> > > >> Reply to this email directly, view it on GitHub
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> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
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> > DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=
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VxNwSxsweOVZ0Bc&s=
> > BbEVTy08p4jXHTT8MLTUH3hJkBu8I-Mnunz9XobiSW4&e=
> > > >,
> > > >> or mute the thread
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> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
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> > oiHL8g02sLNeLWfSJqxjDm1FYrD-VxNwSxsweOVZ0Bc&s=5Zz03_
> > B4lf08At2yh2n930p7xgnE5RAYXydCZFo9RZA&e=
> > > >
> > > >> .
> > > >>
> > > >
> > > >
> > >
> > > —
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>,
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amnona
commented on June 29, 2024
Hi Bishnu,
happy to hear the fix worked :)
Regarding the trim lengths,
based on my experience, the reverse reads tend to have a very high error
rate. Since in the current deblur implementation, a constant error rate is
assumed for all positions, using the reverse reads will force using a high
error correction rate, which will reduce the sensitivity.
Therefore, the default deblur error profile is for the forward reads only.
What I usually do is work only with the forward reads (without merging the
reverse reads). Personally, i also like to work with even shorted reads
(i.e. trim length=200 or 250) again due to the higher error rate at the
ends of long reads. So if you choose this option, just take the forward
reads and use trim length=200 / 250
If you want to keep the merged reverse reads, i would recommend just
concatenating the forward and reverse reads (i.e. if you have 1000 reads,
join the forward and reverse for each of the 1000 reads without merging -
so getting 1000 reads of length 300bp+300bp=600bp). Then running deblur
with trim length 600 and then un-concatenating to 2*300bp reads and then
merging if you want.
If you choose to run deblur on the merged reads instead, remember that all
reads shorter than the trim length will be discarded.
In general, there is a balance between read length (which affects the
phylogenetic resolution) and noise (which affects the ability to tell apart
very close sequences in your sample). Personally i think 250bp is enough
phylogenetic resolution for most scenarios compared to the price you pay
for increased noise. But this is a matter of taste and the specific use
case.
BTW: what sequencing primers did you use (i.e. 515F, 806R etc.)
Let me know how it goes,
Amnon
On Sun, Jul 22, 2018 at 8:55 PM Bishnu Adhikari <[email protected]>
wrote:
… Dear Amnon,
Thank you very much for the information and support. Now, I got the results
and worked perfectly. I want to know your suggeston regarding trim length;
the median sequence length of the reads is 548 since each forward and
reverse reads were 300 bp and joined together. At this condition, what trim
length will be optimum based on your experience?
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Sun, Jul 22, 2018 at 9:46 AM, amnona ***@***.***> wrote:
> Hi Bishnu,
> we have a new dev. version on github that should take care of this bug.
>
> Can you try to install the github version as follows:
> source activate deblurenv
> conda uninstall deblur
> pip install git+git://github.com/biocore/deblur
>
> and then try to run deblur on your data?
> Please let me know if it works now or if the bug is still occurring.
>
> Thanks,
> Amnon
>
> On Thu, Jul 19, 2018 at 9:53 PM Bishnu Adhikari <
***@***.***>
> wrote:
>
> > Dear Amnon,
> >
> >
>
> > Thank you very much for the information. I am eagerly waiting to run it
> > again.
> >
> > Appreciated.
> >
> > Best Regards
> > Bishnu Adhikari
> > PhD Candidate
> > University of Arkansas
> > Poultry Science POSC O-220
> > 1260 W. Maple
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
>
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>>
> Fayetteville, AR 72701
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
> > 4798562305
> >
> > On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***>
> wrote:
> >
> > > Hi,
> > > Should be ready in 24hrs. Will mail when merged and ready for
install.
> > >
> > > Thanks
> > > Amnon
> > >
> > > On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari <
> ***@***.***>
> > >
> > > wrote:
> > >
> > > > Dear Amnon,
> > > >
> > > > Good afternoon,
> > > >
> > > > I am just checking whether bug in the deblur workflow is fixed or
> not.
> > I
> > > > really appreciate you kind support and help.
> > > >
> > > > Thank you
> > > >
> > > > Best Regards
> > > > Bishnu Adhikari
> > > > PhD Candidate
> > > > University of Arkansas
> > > > Poultry Science POSC O-220
> > > > 1260 W. Maple
> <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > >
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >>
> > > Fayetteville, AR 72701
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > > > 4798562305
> > > >
> > > > On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <
> > ***@***.***>
> > > > wrote:
> > > >
> > > > > Dear Amnona,
> > > > >
> > > > > Thank you very much for the information. Please let me know once
it
> > is
> > > > > fixed. I hope it will be fixed soon.
> > > > >
> > > > > Best Regards
> > > > > Bishnu Adhikari
> > > > > PhD Candidate
> > > > > University of Arkansas
> > > > > Poultry Science POSC O-220
> > > > > 1260 W. Maple
> <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > >
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >>
> > > > Fayetteville, AR 72701
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
>
> > >
> > > > > 4798562305
> > > > >
> > > > > On Sat, Jul 14, 2018 at 4:12 PM, amnona <
***@***.***>
> > > > wrote:
> > > > >
> > > > >> Hi Bishnu,
> > > > >> This seems to be a bug in the deblur code due to a change in how
> > > python
> > > > >> treats 1E9 (float rather than int) in new python versions.
> > > > >> We're working on a fix. Will update once it is ready.
> > > > >>
> > > > >> Thanks for the report
> > > > >> Amnon
> > > > >>
> > > > >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> > > > >> ***@***.***>
> > > > >> wrote:
> > > > >>
> > > > >> > Dear Amnon,
> > > > >> >
> > > > >> > Please find the deblur log ran a/c to your suggestions which
> also
> > > got
> > > > >> the
> > > > >> > same error message as above when I gave following command.
> > > > >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp
> > seqs.fna
> > > > >> > --output-dir output -t 400 --log-level 1
> > > > >> >
> > > > >> > deblur.log <
> > > > https://github.com/biocore/deblur/files/2186150/deblur.log>
> > > > >> > Thank you
> > > > >> > Regards
> > > > >> > Bishnu Adhikari
> > > > >> >
> > > > >> > —
> > > > >> > You are receiving this because you commented.
> > > > >> > Reply to this email directly, view it on GitHub
> > > > >> > <#176#
> > > issuecomment-404305789
> > > > >,
> > > > >> or mute
> > > > >> > the thread
> > > > >> > <https://github.com/notifications/unsubscribe-auth/AFkA8qRA4
> > > > >> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
> > > > >>
> > > > >> > .
> > > > >> >
> > > > >>
> > > > >> —
> > > > >> You are receiving this because you authored the thread.
> > > > >> Reply to this email directly, view it on GitHub
> > > > >> <
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> > > com_biocore_deblur_issues_176-23issuecomment-2D405050225&d=
> > > DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=
> > > VdUecPkVFhn38jM8aYFL6Q&m=oiHL8g02sLNeLWfSJqxjDm1FYrD-
> VxNwSxsweOVZ0Bc&s=
> > > BbEVTy08p4jXHTT8MLTUH3hJkBu8I-Mnunz9XobiSW4&e=
> > > > >,
> > > > >> or mute the thread
> > > > >> <
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> > > com_notifications_unsubscribe-2Dauth_ARVbfi2xVtM1sgmPxd4PSAHUl-
> > > 5FDkTO5xks5uGl7NgaJpZM4VLYwz&d=DwMFaQ&c=7ypwAowFJ8v-mw8AB-
> > > SdSueVQgSDL4HiiSaLK01W8HA&r=VdUecPkVFhn38jM8aYFL6Q&m=
> > > oiHL8g02sLNeLWfSJqxjDm1FYrD-VxNwSxsweOVZ0Bc&s=5Zz03_
> > > B4lf08At2yh2n930p7xgnE5RAYXydCZFo9RZA&e=
> > > > >
> > > > >> .
> > > > >>
> > > > >
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub
> > > > <
#176 (comment)
> >,
> > > or mute
> > > > the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AFkA8irvfs_
> > > vPcl0ngYQ3xQoiuQKCmv1ks5uINOLgaJpZM4VLYwz>
> > >
> > > > .
> > > >
> > >
> > > —
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> > > Reply to this email directly, view it on GitHub
> > > <
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_biocore_deblur_issues_176-23issuecomment-2D406377880&d=
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> > >,
> > > or mute the thread
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> com_notifications_unsubscribe-2Dauth_ARVbflrV1jZuLYhQ6Kuqh142cl-
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> 8Iu3onnk9iM1Mc3omoGcyuq1uxn3jWmVYO5kxry5S_0&e=
> > >
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#176 (comment)>,
> or mute
> > the thread
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> auth/AFkA8mS_17usj8nJYfy7gFD_FPlbxQ6nks5uINW8gaJpZM4VLYwz>
>
> > .
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>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <
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.
from deblur.
bishnuadhikari
commented on June 29, 2024
Dear Amnon,
Good morning!
Thank you very much for your suggestions. I have used different primer sets
(27F and 533R) and have barcodes (4nt) on both forward and reverse reads as
shown in the attached image. I have to join them and extract barcodes in
order to demultiplex them. I sought whether QIIME2 has developed piplelines
for such type of library, but didn't succeed. So, I found using deblur
workflow outside QIIME2 from the sequences that I got from
split_libraries_fastq.py option of QIIME1 and importing the output of
deblur later will be the best choice so far?, based on my research. I did
quality filtering using trimmomatic and the reads also passed quality score
20 during demultiplexing step. Do you have any suggestions for this type of
sequence that are already joined and demultiplexed? I appreciate your
suggestions and willingness to help.
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
…On Mon, Jul 23, 2018 at 4:46 AM, amnona ***@***.***> wrote:
Hi Bishnu,
happy to hear the fix worked :)
Regarding the trim lengths,
based on my experience, the reverse reads tend to have a very high error
rate. Since in the current deblur implementation, a constant error rate is
assumed for all positions, using the reverse reads will force using a high
error correction rate, which will reduce the sensitivity.
Therefore, the default deblur error profile is for the forward reads only.
What I usually do is work only with the forward reads (without merging the
reverse reads). Personally, i also like to work with even shorted reads
(i.e. trim length=200 or 250) again due to the higher error rate at the
ends of long reads. So if you choose this option, just take the forward
reads and use trim length=200 / 250
If you want to keep the merged reverse reads, i would recommend just
concatenating the forward and reverse reads (i.e. if you have 1000 reads,
join the forward and reverse for each of the 1000 reads without merging -
so getting 1000 reads of length 300bp+300bp=600bp). Then running deblur
with trim length 600 and then un-concatenating to 2*300bp reads and then
merging if you want.
If you choose to run deblur on the merged reads instead, remember that all
reads shorter than the trim length will be discarded.
In general, there is a balance between read length (which affects the
phylogenetic resolution) and noise (which affects the ability to tell apart
very close sequences in your sample). Personally i think 250bp is enough
phylogenetic resolution for most scenarios compared to the price you pay
for increased noise. But this is a matter of taste and the specific use
case.
BTW: what sequencing primers did you use (i.e. 515F, 806R etc.)
Let me know how it goes,
Amnon
On Sun, Jul 22, 2018 at 8:55 PM Bishnu Adhikari ***@***.***>
wrote:
> Dear Amnon,
>
> Thank you very much for the information and support. Now, I got the
results
> and worked perfectly. I want to know your suggeston regarding trim
length;
> the median sequence length of the reads is 548 since each forward and
> reverse reads were 300 bp and joined together. At this condition, what
trim
> length will be optimum based on your experience?
>
> Thank you
>
> Best Regards
> Bishnu Adhikari
> PhD Candidate
> University of Arkansas
> Poultry Science POSC O-220
> 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>>
Fayetteville, AR 72701
<https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g>
> 4798562305
>
> On Sun, Jul 22, 2018 at 9:46 AM, amnona ***@***.***>
wrote:
>
> > Hi Bishnu,
> > we have a new dev. version on github that should take care of this bug.
> >
> > Can you try to install the github version as follows:
> > source activate deblurenv
> > conda uninstall deblur
> > pip install git+git://github.com/biocore/deblur
> >
> > and then try to run deblur on your data?
> > Please let me know if it works now or if the bug is still occurring.
> >
> > Thanks,
> > Amnon
> >
> > On Thu, Jul 19, 2018 at 9:53 PM Bishnu Adhikari <
> ***@***.***>
> > wrote:
> >
> > > Dear Amnon,
> > >
> > >
> >
> > > Thank you very much for the information. I am eagerly waiting to run
it
> > > again.
> > >
> > > Appreciated.
> > >
> > > Best Regards
> > > Bishnu Adhikari
> > > PhD Candidate
> > > University of Arkansas
> > > Poultry Science POSC O-220
> > > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> >
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >>
> > Fayetteville, AR 72701
> > <
> https://maps.google.com/?q=1260+W.+Maple+%0A+
Fayetteville,+AR+72701&entry=gmail&source=g
> >
> > > 4798562305
> > >
> > > On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***>
> > wrote:
> > >
> > > > Hi,
> > > > Should be ready in 24hrs. Will mail when merged and ready for
> install.
> > > >
> > > > Thanks
> > > > Amnon
> > > >
> > > > On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari <
> > ***@***.***>
> > > >
> > > > wrote:
> > > >
> > > > > Dear Amnon,
> > > > >
> > > > > Good afternoon,
> > > > >
> > > > > I am just checking whether bug in the deblur workflow is fixed or
> > not.
> > > I
> > > > > really appreciate you kind support and help.
> > > > >
> > > > > Thank you
> > > > >
> > > > > Best Regards
> > > > > Bishnu Adhikari
> > > > > PhD Candidate
> > > > > University of Arkansas
> > > > > Poultry Science POSC O-220
> > > > > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> > > >
> > > >
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> > > >>
> > > > Fayetteville, AR 72701
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> > > >
> > > > > 4798562305
> > > > >
> > > > > On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <
> > > ***@***.***>
> > > > > wrote:
> > > > >
> > > > > > Dear Amnona,
> > > > > >
> > > > > > Thank you very much for the information. Please let me know
once
> it
> > > is
> > > > > > fixed. I hope it will be fixed soon.
> > > > > >
> > > > > > Best Regards
> > > > > > Bishnu Adhikari
> > > > > > PhD Candidate
> > > > > > University of Arkansas
> > > > > > Poultry Science POSC O-220
> > > > > > 1260 W. Maple
<https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> > > >
> > > >
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> > > >>
> > > > > Fayetteville, AR 72701
> > > > <
> > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > Fayetteville,+AR+72701&entry=gmail&source=g
> >
> > > >
> > > > > > 4798562305
> > > > > >
> > > > > > On Sat, Jul 14, 2018 at 4:12 PM, amnona <
> ***@***.***>
> > > > > wrote:
> > > > > >
> > > > > >> Hi Bishnu,
> > > > > >> This seems to be a bug in the deblur code due to a change in
how
> > > > python
> > > > > >> treats 1E9 (float rather than int) in new python versions.
> > > > > >> We're working on a fix. Will update once it is ready.
> > > > > >>
> > > > > >> Thanks for the report
> > > > > >> Amnon
> > > > > >>
> > > > > >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> > > > > >> ***@***.***>
> > > > > >> wrote:
> > > > > >>
> > > > > >> > Dear Amnon,
> > > > > >> >
> > > > > >> > Please find the deblur log ran a/c to your suggestions which
> > also
> > > > got
> > > > > >> the
> > > > > >> > same error message as above when I gave following command.
> > > > > >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp
> > > seqs.fna
> > > > > >> > --output-dir output -t 400 --log-level 1
> > > > > >> >
> > > > > >> > deblur.log <
> > > > > https://github.com/biocore/deblur/files/2186150/deblur.log>
> > > > > >> > Thank you
> > > > > >> > Regards
> > > > > >> > Bishnu Adhikari
> > > > > >> >
> > > > > >> > —
> > > > > >> > You are receiving this because you commented.
> > > > > >> > Reply to this email directly, view it on GitHub
> > > > > >> > <#176#
> > > > issuecomment-404305789
> > > > > >,
> > > > > >> or mute
> > > > > >> > the thread
> > > > > >> > <https://github.com/notifications/unsubscribe-
auth/AFkA8qRA4
> > > > > >> DqQgxNikMgLTo4SRhNyh-Tmks5uFmXXgaJpZM4VLYwz>
> > > > > >>
> > > > > >> > .
> > > > > >> >
> > > > > >>
> > > > > >> —
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> > > > > >> Reply to this email directly, view it on GitHub
> > > > > >> <
> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> > > > com_biocore_deblur_issues_176-23issuecomment-2D405050225&d=
> > > > DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=
> > > > VdUecPkVFhn38jM8aYFL6Q&m=oiHL8g02sLNeLWfSJqxjDm1FYrD-
> > VxNwSxsweOVZ0Bc&s=
> > > > BbEVTy08p4jXHTT8MLTUH3hJkBu8I-Mnunz9XobiSW4&e=
> > > > > >,
> > > > > >> or mute the thread
> > > > > >> <
> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> > > > com_notifications_unsubscribe-2Dauth_ARVbfi2xVtM1sgmPxd4PSAHUl-
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> > > > SdSueVQgSDL4HiiSaLK01W8HA&r=VdUecPkVFhn38jM8aYFL6Q&m=
> > > > oiHL8g02sLNeLWfSJqxjDm1FYrD-VxNwSxsweOVZ0Bc&s=5Zz03_
> > > > B4lf08At2yh2n930p7xgnE5RAYXydCZFo9RZA&e=
> > > > > >
> > > > > >> .
> > > > > >>
> > > > > >
> > > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you commented.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <
> #176 (comment)
> > >,
> > > > or mute
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> > > >
> > > > > .
> > > > >
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from deblur.
amnona
commented on June 29, 2024
Hi Bishnu,
I don't know a lot about qiime2 - maybe best to ask in the qiime2 forum
about the sort of data you start with (probably the qiime2 developers will
be happy to hear about new inputs and how to incorporate into qiime2
pipelin2).
currently, the steps you mentioned (preprocessing in qiime1 and then
running deblur standalone and then importing to qiime2) make sense (i
sometimes use a similar general approach). Quality filtering to 20 is good.
In general, if you process after the pair-merging, you risk ignoring
bacteria where the amplified region size is bigger than (600 - overlap
requirement). I don't know if this is a concern for the region you are
sequencing and in any case, amplicon sequencing does not capture all
bacteria, so this is not a show stopper.
I would recommend deblurring to length 200 or 250, but maybe best option is
to try different trim lengths (i.e. 200,250 and 500) and compare the
results so see what payoff you have between read length and error rate.
On Mon, Jul 23, 2018 at 5:17 PM Bishnu Adhikari <[email protected]>
wrote:
… Dear Amnon,
Good morning!
Thank you very much for your suggestions. I have used different primer sets
(27F and 533R) and have barcodes (4nt) on both forward and reverse reads as
shown in the attached image. I have to join them and extract barcodes in
order to demultiplex them. I sought whether QIIME2 has developed piplelines
for such type of library, but didn't succeed. So, I found using deblur
workflow outside QIIME2 from the sequences that I got from
split_libraries_fastq.py option of QIIME1 and importing the output of
deblur later will be the best choice so far?, based on my research. I did
quality filtering using trimmomatic and the reads also passed quality score
20 during demultiplexing step. Do you have any suggestions for this type of
sequence that are already joined and demultiplexed? I appreciate your
suggestions and willingness to help.
Thank you
Best Regards
Bishnu Adhikari
PhD Candidate
University of Arkansas
Poultry Science POSC O-220
1260 W. Maple
Fayetteville, AR 72701
4798562305
On Mon, Jul 23, 2018 at 4:46 AM, amnona ***@***.***> wrote:
> Hi Bishnu,
> happy to hear the fix worked :)
>
> Regarding the trim lengths,
> based on my experience, the reverse reads tend to have a very high error
> rate. Since in the current deblur implementation, a constant error rate
is
> assumed for all positions, using the reverse reads will force using a
high
> error correction rate, which will reduce the sensitivity.
> Therefore, the default deblur error profile is for the forward reads
only.
> What I usually do is work only with the forward reads (without merging
the
> reverse reads). Personally, i also like to work with even shorted reads
> (i.e. trim length=200 or 250) again due to the higher error rate at the
> ends of long reads. So if you choose this option, just take the forward
> reads and use trim length=200 / 250
> If you want to keep the merged reverse reads, i would recommend just
> concatenating the forward and reverse reads (i.e. if you have 1000 reads,
> join the forward and reverse for each of the 1000 reads without merging -
> so getting 1000 reads of length 300bp+300bp=600bp). Then running deblur
> with trim length 600 and then un-concatenating to 2*300bp reads and then
> merging if you want.
> If you choose to run deblur on the merged reads instead, remember that
all
> reads shorter than the trim length will be discarded.
>
> In general, there is a balance between read length (which affects the
> phylogenetic resolution) and noise (which affects the ability to tell
apart
> very close sequences in your sample). Personally i think 250bp is enough
> phylogenetic resolution for most scenarios compared to the price you pay
> for increased noise. But this is a matter of taste and the specific use
> case.
>
> BTW: what sequencing primers did you use (i.e. 515F, 806R etc.)
>
> Let me know how it goes,
> Amnon
>
>
> On Sun, Jul 22, 2018 at 8:55 PM Bishnu Adhikari <
***@***.***>
>
> wrote:
>
> > Dear Amnon,
> >
> > Thank you very much for the information and support. Now, I got the
> results
> > and worked perfectly. I want to know your suggeston regarding trim
> length;
> > the median sequence length of the reads is 548 since each forward and
> > reverse reads were 300 bp and joined together. At this condition, what
> trim
> > length will be optimum based on your experience?
> >
> > Thank you
> >
> > Best Regards
> > Bishnu Adhikari
> > PhD Candidate
> > University of Arkansas
> > Poultry Science POSC O-220
> > 1260 W. Maple
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
>
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>>
> Fayetteville, AR 72701
> <
https://maps.google.com/?q=1260+W.+Maple+%0A+Fayetteville,+AR+72701&entry=gmail&source=g
>
> > 4798562305
> >
> > On Sun, Jul 22, 2018 at 9:46 AM, amnona ***@***.***>
> wrote:
> >
> > > Hi Bishnu,
> > > we have a new dev. version on github that should take care of this
bug.
> > >
> > > Can you try to install the github version as follows:
> > > source activate deblurenv
> > > conda uninstall deblur
> > > pip install git+git://github.com/biocore/deblur
> > >
> > > and then try to run deblur on your data?
> > > Please let me know if it works now or if the bug is still occurring.
> > >
> > > Thanks,
> > > Amnon
> > >
> > > On Thu, Jul 19, 2018 at 9:53 PM Bishnu Adhikari <
> > ***@***.***>
> > > wrote:
> > >
> > > > Dear Amnon,
> > > >
> > > >
> > >
> > > > Thank you very much for the information. I am eagerly waiting to
run
> it
> > > > again.
> > > >
> > > > Appreciated.
> > > >
> > > > Best Regards
> > > > Bishnu Adhikari
> > > > PhD Candidate
> > > > University of Arkansas
> > > > Poultry Science POSC O-220
> > > > 1260 W. Maple
> <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > >
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >>
> > > Fayetteville, AR 72701
> > > <
> > https://maps.google.com/?q=1260+W.+Maple+%0A+
> Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > > > 4798562305
> > > >
> > > > On Thu, Jul 19, 2018 at 1:49 PM, amnona ***@***.***>
> > > wrote:
> > > >
> > > > > Hi,
> > > > > Should be ready in 24hrs. Will mail when merged and ready for
> > install.
> > > > >
> > > > > Thanks
> > > > > Amnon
> > > > >
> > > > > On Thu, Jul 19, 2018, 9:44 PM Bishnu Adhikari <
> > > ***@***.***>
> > > > >
> > > > > wrote:
> > > > >
> > > > > > Dear Amnon,
> > > > > >
> > > > > > Good afternoon,
> > > > > >
> > > > > > I am just checking whether bug in the deblur workflow is fixed
or
> > > not.
> > > > I
> > > > > > really appreciate you kind support and help.
> > > > > >
> > > > > > Thank you
> > > > > >
> > > > > > Best Regards
> > > > > > Bishnu Adhikari
> > > > > > PhD Candidate
> > > > > > University of Arkansas
> > > > > > Poultry Science POSC O-220
> > > > > > 1260 W. Maple
> <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > > > >
> > > > >
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > > > >>
> > > > > Fayetteville, AR 72701
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > > > >
> > > > > > 4798562305
> > > > > >
> > > > > > On Mon, Jul 16, 2018 at 2:53 PM, Bishnu Adhikari <
> > > > ***@***.***>
> > > > > > wrote:
> > > > > >
> > > > > > > Dear Amnona,
> > > > > > >
> > > > > > > Thank you very much for the information. Please let me know
> once
> > it
> > > > is
> > > > > > > fixed. I hope it will be fixed soon.
> > > > > > >
> > > > > > > Best Regards
> > > > > > > Bishnu Adhikari
> > > > > > > PhD Candidate
> > > > > > > University of Arkansas
> > > > > > > Poultry Science POSC O-220
> > > > > > > 1260 W. Maple
> <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > <https://maps.google.com/?q=1260+W.+Maple&entry=gmail&source=g>
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > > > >
> > > > >
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > > > >>
> > > > > > Fayetteville, AR 72701
> > > > > <
> > > > https://maps.google.com/?q=1260+W.+Maple+%0A+
>
> > > Fayetteville,+AR+72701&entry=gmail&source=g
> > >
> > > > >
> > > > > > > 4798562305
> > > > > > >
> > > > > > > On Sat, Jul 14, 2018 at 4:12 PM, amnona <
> > ***@***.***>
> > > > > > wrote:
> > > > > > >
> > > > > > >> Hi Bishnu,
> > > > > > >> This seems to be a bug in the deblur code due to a change in
> how
> > > > > python
> > > > > > >> treats 1E9 (float rather than int) in new python versions.
> > > > > > >> We're working on a fix. Will update once it is ready.
> > > > > > >>
> > > > > > >> Thanks for the report
> > > > > > >> Amnon
> > > > > > >>
> > > > > > >> On Wed, Jul 11, 2018 at 11:53 PM Bishnu Adhikari <
> > > > > > >> ***@***.***>
> > > > > > >> wrote:
> > > > > > >>
> > > > > > >> > Dear Amnon,
> > > > > > >> >
> > > > > > >> > Please find the deblur log ran a/c to your suggestions
which
> > > also
> > > > > got
> > > > > > >> the
> > > > > > >> > same error message as above when I gave following command.
> > > > > > >> > (deblurenv) ***@***.***:~$ deblur workflow --seqs-fp
> > > > seqs.fna
> > > > > > >> > --output-dir output -t 400 --log-level 1
> > > > > > >> >
> > > > > > >> > deblur.log <
> > > > > > https://github.com/biocore/deblur/files/2186150/deblur.log>
> > > > > > >> > Thank you
> > > > > > >> > Regards
> > > > > > >> > Bishnu Adhikari
> > > > > > >> >
> > > > > > >> > —
> > > > > > >> > You are receiving this because you commented.
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wasade
commented on June 29, 2024
Closing as the seed issue of casting 1E9 has been addressed.
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