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raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided? #16
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Hi, Cheers |
Had same problem here on Crispa example. I installed using docker.
It seems to stop when aligning transcripts using GMAP. I then tried appending
It did not swap to minimap and encounter the same error? |
No queries were passed to GMAP and the file size of |
Working on it. I will write ASAP i will find the problem |
Dear @cgjosephlee and @ncgrjsmiao ,
please let me know if it works that i came move this as default image |
Hi @lfaino , Best |
We need to check if mysql started. you can test this by running:
you should be in mysql. if you get an error, let me know |
Gocha!
|
do you have installed mysql on your system? |
Yes, but it seems that I cannot access it since I have no root privilege.
|
Hi @cgjosephlee , please let me know. Cheers |
With this docker://lfaino/lorean:noiIPRS, running Singularity 3.1.0 `cp: cannot stat '/db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run/PASA/annotation.pasa_assemblies.gff3': No such file or directory During handling of the above exception, another exception occurred: Traceback (most recent call last): |
Exit at "MOVING IMPORTANT FILES" ###PASA STARTS AT: 08:09:28 06-04 ### ###AUGUSTUS, GENEMARK-ES AND AAT STARTED AT:08:47:55 06-04 ### ###EVM STARTED AT: 14:29:52 06-04 ### |
Hi @cgjosephlee , Cheers |
ls -l /db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run/PASA/: drwxr-xr-x 8 ncgr ncgr 4096 Apr 6 16:47 ./ |
is this the output after that you re-downloaded the image? |
|
This is the output after I download this image
docker://lfaino/lorean:noiIPRS firstly
Could you tell me that the differences between docker://lfaino/lorean
and docker://lfaino/lorean:noiIPRS?
…On Sun, Apr 7, 2019 at 3:47 AM Luigi Faino ***@***.***> wrote:
is this the output after that you re-downloaded the image?
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I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS. it was a mistake from my side. The latest image is called docker://lfaino/lorean:noIPRS.
these are the main changes. Sorry for the problem with the naming. |
Thank for your good job and quick reply. Now I re-download
docker://lfaino/lorean:noIPRS, then re-run my job.
Tomorrow I will tell you my result of running lorean:noIPRS!
Best regards!
…On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino ***@***.***> wrote:
I saw an old error (on my side) in your images: the image is not anymore
docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you
notice, there is not anymore the i before IPRS. it was a mistake from my
side. The latest image is called docker://lfaino/lorean:noIPRS.
There are few differences between docker://lfaino/lorean and
docker://lfaino/lorean:noIPRS:
1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this
was a pain before because LoReAn need to start a service in the image and
it is a bit difficult on some host systems. now PASA uses sqlite and it is
managed better by the image
2. I update GeneMark. now i have the latest version in
docker://lfaino/lorean:noIPRS
3. gffread tool was updated and few change need to be made to use the
new version in docker://lfaino/lorean:noIPRS
these are the main changes.
Sorry for the problem with the naming.
Please dowload the new version using
docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER
$UID
and test again
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Using the image docker://lfaino/lorean:noIPRS
Errors as follows:
###RUNNING iASSEMBLER 02:07:27 08-04 ###
Traceback (most recent call last):
File "/opt/LoReAn/code//lorean.py", line 563, in <module>
main()
File "/opt/LoReAn/code//lorean.py", line 440, in main
adapter_value, threads_use, args.adapter_match_score, ref_rename,
UnboundLocalError: local variable 'adapter_value' referenced before
assignment
How to fix it ? Thanks a lot!
…On Sun, Apr 7, 2019 at 10:56 PM Smith Waterman ***@***.***> wrote:
Thank for your good job and quick reply. Now I re-download
docker://lfaino/lorean:noIPRS, then re-run my job.
Tomorrow I will tell you my result of running lorean:noIPRS!
Best regards!
On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino ***@***.***>
wrote:
> I saw an old error (on my side) in your images: the image is not anymore
> docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you
> notice, there is not anymore the i before IPRS. it was a mistake from my
> side. The latest image is called docker://lfaino/lorean:noIPRS.
> There are few differences between docker://lfaino/lorean and
> docker://lfaino/lorean:noIPRS:
>
> 1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this
> was a pain before because LoReAn need to start a service in the image and
> it is a bit difficult on some host systems. now PASA uses sqlite and it is
> managed better by the image
> 2. I update GeneMark. now i have the latest version in
> docker://lfaino/lorean:noIPRS
> 3. gffread tool was updated and few change need to be made to use the
> new version in docker://lfaino/lorean:noIPRS
>
> these are the main changes.
>
> Sorry for the problem with the naming.
> Please dowload the new version using
> docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py
> $USER $UID
> and test again
>
> —
> You are receiving this because you commented.
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> <#16 (comment)>, or mute
> the thread
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> .
>
|
My running command list is : " nohup lorean.py -a -rp repeats.fix.bed -sr
clean_R_1.fastq,clean_R_2.fastq -lr Long.fasta -pr rice_bamboo_prot.fasta
-sp bamboo test_scaffold.fa -d -f -mg -t 4 --keep_tmp 1>1.out 2>2.out &"
…On Mon, Apr 8, 2019 at 2:36 PM Smith Waterman ***@***.***> wrote:
Using the image docker://lfaino/lorean:noIPRS
Errors as follows:
###RUNNING iASSEMBLER 02:07:27 08-04 ###
Traceback (most recent call last):
File "/opt/LoReAn/code//lorean.py", line 563, in <module>
main()
File "/opt/LoReAn/code//lorean.py", line 440, in main
adapter_value, threads_use, args.adapter_match_score, ref_rename,
UnboundLocalError: local variable 'adapter_value' referenced before
assignment
How to fix it ? Thanks a lot!
On Sun, Apr 7, 2019 at 10:56 PM Smith Waterman ***@***.***> wrote:
> Thank for your good job and quick reply. Now I re-download
> docker://lfaino/lorean:noIPRS, then re-run my job.
> Tomorrow I will tell you my result of running lorean:noIPRS!
>
> Best regards!
>
> On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino ***@***.***>
> wrote:
>
>> I saw an old error (on my side) in your images: the image is not anymore
>> docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you
>> notice, there is not anymore the i before IPRS. it was a mistake from my
>> side. The latest image is called docker://lfaino/lorean:noIPRS.
>> There are few differences between docker://lfaino/lorean and
>> docker://lfaino/lorean:noIPRS:
>>
>> 1. docker://lfaino/lorean:noIPRS does not require mysql anymore.
>> this was a pain before because LoReAn need to start a service in the image
>> and it is a bit difficult on some host systems. now PASA uses sqlite and it
>> is managed better by the image
>> 2. I update GeneMark. now i have the latest version in
>> docker://lfaino/lorean:noIPRS
>> 3. gffread tool was updated and few change need to be made to use
>> the new version in docker://lfaino/lorean:noIPRS
>>
>> these are the main changes.
>>
>> Sorry for the problem with the naming.
>> Please dowload the new version using
>> docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py
>> $USER $UID
>> and test again
>>
>> —
>> You are receiving this because you commented.
>> Reply to this email directly, view it on GitHub
>> <#16 (comment)>, or mute
>> the thread
>> <https://github.com/notifications/unsubscribe-auth/AOSBuAphjSMpD5D2DZ_zA8xW2VwbQzs-ks5veZiRgaJpZM4cLtZj>
>> .
>>
>
|
The easiest way is to provide a file with the adapter sequence. Are you using PacBio or Nanopore data? |
Still no luck after re-download latest image. I doubt it was stuck at trinity stage.
|
do you mind to share your test data? I will test and see if i can find the error and fix it |
The test data is |
@cgjosephlee ok. |
@zcrself; |
Because this my first running, why it has these errors: GMAP database
existed already?
###MAPPING CONSENSUS ASSEMBLIES 23:38:48 09-04 ###
###GMAP MAPPING STARTED AT: 23:38:48 09-04 ###
###BUILD INDEX###
GMAP database existed already:
/db2/ncgr/mytest/LoReAn_annotation/run/gmap_output/test_scaffold.fa.masked.fasta.rename.fasta_GMAPindex
--- skipping
…On Wed, Apr 10, 2019 at 9:08 AM Smith Waterman ***@***.***> wrote:
I have tested the new image, The Previous errors disappear, the new
error occurs. Are there any questions about my test data. I can give my
test data to you!
NAME DATE CREATED SIZE TYPE
lorean_noIPRS.sif 2019-04-09 22:41:37(Shanghai Time) 3.31 Gb
oci
- |# | 0 Elapsed Time:
0:00:00
Traceback (most recent call last):
File "/opt/LoReAn/code/lorean.py", line 564, in <module>
main()
File "/opt/LoReAn/code/lorean.py", line 506, in main
args.verbose, Fflag=True)
File "/opt/LoReAn/code/mapping.py", line 400, in gmap
wd, Fflag, type_out, verbose)
File "/opt/LoReAn/code/mapping.py", line 131, in gmap_map
filename = longest_cds(list_fasta[0][1], list_fasta[1][1], verbose,
working_dir, filename)
File "/opt/LoReAn/code/mapping.py", line 189, in longest_cds
db = gffutils.create_db(gff_file, ':memory:',
merge_strategy='create_unique', keep_order=True, transform=transform)
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line
1288, in create_db
c.create()
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line
504, in create
self._populate_from_lines(self.iterator)
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line
625, in _populate_from_lines
raise ValueError("No lines parsed -- was an empty file provided?")
ValueError: No lines parsed -- was an empty file provided?
On Tue, Apr 9, 2019 at 9:43 PM Luigi Faino ***@***.***>
wrote:
> The images is ready. Can you please test it?
>
> thanks for the patience
>
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>
|
@zcrself , |
There are six files in my command line.
1. http://db.ncgr.ac.cn/doc/test_sr_1.fastq.gz
2. http://db.ncgr.ac.cn/doc/test_sr_2.fastq.gz
3. http://db.ncgr.ac.cn/doc/test_scaffold.fa.gz
4. http://db.ncgr.ac.cn/doc/rice_bamboo_prot.fasta.gz
5. http://db.ncgr.ac.cn/doc/repeats.fix.bed.gz
6. http://db.ncgr.ac.cn/doc/Long.fasta.gz
My command line is
lorean -rp repeats.fix.bed -sr test_sr_1.fastq,test_sr_2.fastq -lr
Long.fasta -pr rice_bamboo_prot.fasta -sp rice test_scaffold.fa -t 4
--keep_tmp
Thanks for your wonderful work!
…On Wed, Apr 10, 2019 at 1:58 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
it would be nice. Can you please send to me? additionally, can you send me
the command that you run and some info on the system that you are using.
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|
My system info:
OS: Ubuntu 16.04.5 LTS x86_64
RAM: 94G
CPU: Intel(R) Xeon(R) CPU X5560 @ 2.80GHz
CPU(s): 4
Disk: 2T RAID10
singularity version 3.1.0
…On Wed, Apr 10, 2019 at 1:58 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
it would be nice. Can you please send to me? additionally, can you send me
the command that you run and some info on the system that you are using.
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|
@zcrself |
singularity shell
…On Wed, Apr 10, 2019 at 6:23 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
Do you use singularity exe or singularity shell?
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Could you help me to run lorean using my data which I have sent to you
…On Wed, Apr 10, 2019 at 7:37 PM Smith Waterman ***@***.***> wrote:
singularity shell
On Wed, Apr 10, 2019 at 6:23 PM Luigi Faino ***@***.***>
wrote:
> @zcrself <https://github.com/zcrself>
> Do you use singularity exe or singularity shell?
>
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>
|
@zcrself |
*very appreciated!*
…On Wed, Apr 10, 2019 at 7:39 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
already testing. I will let you now
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@zcrself Cheers |
great! Thank you for helping me !
…On Thursday, April 11, 2019, Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
the problem was that you provided the long reads file as a ".fasta" file
but actually is a fastq file.
LoReAn got confused.
this was the problem.
Cheers
Luigi
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After renaming Long.fasta to Long.fastq, I will test my command line, then
I will tell you the result of running
…On Thu, Apr 11, 2019 at 3:05 AM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
the problem was that you provided the long reads file as a ".fasta" file
but actually is a fastq file.
LoReAn got confused.
this was the problem.
Cheers
Luigi
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After renaming Long.fasta to Long.fastq, have you tested the command line.
Is everything OK?
…On Thu, Apr 11, 2019 at 9:37 AM Smith Waterman ***@***.***> wrote:
After renaming Long.fasta to Long.fastq, I will test my command line,
then I will tell you the result of running
On Thu, Apr 11, 2019 at 3:05 AM Luigi Faino ***@***.***>
wrote:
> @zcrself <https://github.com/zcrself>
> the problem was that you provided the long reads file as a ".fasta" file
> but actually is a fastq file.
> LoReAn got confused.
> this was the problem.
>
> Cheers
> Luigi
>
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>
|
@zcrself Cheers |
@cgjosephlee @zcrself i will wait your feedback |
Now I am testing the new image lfaino/lorean:noIPRS, some hours later I
will tell you the result.
…On Thu, Apr 11, 2019 at 3:32 PM Luigi Faino ***@***.***> wrote:
@cgjosephlee <https://github.com/cgjosephlee> @zcrself
<https://github.com/zcrself>
did you test the new image? did it work? can I move the noIPRS image to
the production image?
i will wait your feedback
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Great news.
…On Thu, Apr 11, 2019 at 3:31 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
Yes it did finish. if you restart a run, please remove the gmap and
consensus folders from the run
Cheers
Luigi
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I have the example run successfully. Thank you! |
Great job. I have finished my test data.
Your new image is OK!
…On Thu, Apr 11, 2019 at 3:32 PM Luigi Faino ***@***.***> wrote:
@cgjosephlee <https://github.com/cgjosephlee> @zcrself
<https://github.com/zcrself>
did you test the new image? did it work? can I move the noIPRS image to
the production image?
i will wait your feedback
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@cgjosephlee @zcrself @ncgrjsmiao , Cheers |
Using test data, gff3 have generated!
I have reviewed the result, it is not ideal, I think that the reason is the
size of RNA-seq is small
I will inscrease the size of RNA-seq, then re-run it
…On Wed, Apr 17, 2019 at 1:59 PM Luigi Faino ***@***.***> wrote:
@cgjosephlee <https://github.com/cgjosephlee> @zcrself
<https://github.com/zcrself> @ncgrjsmiao <https://github.com/ncgrjsmiao> ,
Can i close this issue? can you please give me a feedback on the
annotation that you generate with your own data? is it any good?
Cheers
Luigi
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Still had no luck on my data, maybe I'll try it again when I have time. |
Traceback (most recent call last):
File "/opt/LoReAn/code//lorean.py", line 564, in <module>
main()
File "/opt/LoReAn/code//lorean.py", line 188, in main
args.verbose, Fflag=True)
File "/opt/LoReAn/code/mapping.py", line 400, in gmap
wd, Fflag, type_out, verbose)
File "/opt/LoReAn/code/mapping.py", line 65, in gmap_map
record_dict = parse_fasta(reads)
File "/opt/LoReAn/code/mapping.py", line 173, in parse_fasta
with open(fasta, "r") as fh:
FileNotFoundError: [Errno 2] No such file or directory:
'/db2/ncgr/maozhu/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta'
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w'
encoding='UTF-8'>
OSError: [Errno 28] No space left on device
According to this "No space left" error,
after I extend the size of my disk, Maybe I continue to run my lorean,
Need I delete some directory or files ?
…On Wed, Apr 17, 2019 at 1:59 PM Luigi Faino ***@***.***> wrote:
@cgjosephlee <https://github.com/cgjosephlee> @zcrself
<https://github.com/zcrself> @ncgrjsmiao <https://github.com/ncgrjsmiao> ,
Can i close this issue? can you please give me a feedback on the
annotation that you generate with your own data? is it any good?
Cheers
Luigi
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@ncgrjsmiao you can keep the AAT folder, but i would suggest to clean all. Cheers |
In folder "/db3/ncgr/maozhu/LoReAn_annotation/run/split"
find ./ -iname "*.fasta" |wc -l
The result is "277278"
find ./ -iname "*.log" |wc -l
272696
Via 'top' command, why only one AAT is running?
Formerly the server can run many AAT jobs at the same time.
Ubuntu 16.04.5 LTS, 36cpus 72G memory 2T disk at amazonaws
…On Wed, Apr 24, 2019 at 7:14 PM Luigi Faino ***@***.***> wrote:
@ncgrjsmiao <https://github.com/ncgrjsmiao> you can keep the AAT folder,
but i would suggest to clean all.
Cheers
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[image: Screen Shot 2019-04-27 at 20.53.53.png]
…On Sat, Apr 27, 2019 at 9:01 PM Smith Waterman ***@***.***> wrote:
In folder "/db3/ncgr/maozhu/LoReAn_annotation/run/split"
find ./ -iname "*.fasta" |wc -l
The result is "277278"
find ./ -iname "*.log" |wc -l
272696
Via 'top' command, why only one AAT is running?
Formerly the server can run many AAT jobs at the same time.
Ubuntu 16.04.5 LTS, 36cpus 72G memory 2T disk at amazonaws
On Wed, Apr 24, 2019 at 7:14 PM Luigi Faino ***@***.***>
wrote:
> @ncgrjsmiao <https://github.com/ncgrjsmiao> you can keep the AAT folder,
> but i would suggest to clean all.
>
> Cheers
>
> —
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|
*My command line is " lorean.py <http://lorean.py/> -rp repeats.fix.bed -sr
SR_1.fastq,SR_2.fastq -lr Long.fasta -pr all_pep.fasta -sp rice
P_heterocycla_v1_Scaffolds_Poaceae_masked.fa -t 36 --keep_tmp 1>1.out
2>2.out &"*
*There are 36 CPUs on my server, now only one 'nap' job is on running*
*What is the reason?*
…On Sat, Apr 27, 2019 at 9:33 PM Smith Waterman ***@***.***> wrote:
[image: Screen Shot 2019-04-27 at 20.53.53.png]
On Sat, Apr 27, 2019 at 9:01 PM Smith Waterman ***@***.***> wrote:
> In folder "/db3/ncgr/maozhu/LoReAn_annotation/run/split"
>
> find ./ -iname "*.fasta" |wc -l
>
> The result is "277278"
>
>
> find ./ -iname "*.log" |wc -l
>
> 272696
>
>
>
> Via 'top' command, why only one AAT is running?
>
> Formerly the server can run many AAT jobs at the same time.
>
>
> Ubuntu 16.04.5 LTS, 36cpus 72G memory 2T disk at amazonaws
>
>
>
> On Wed, Apr 24, 2019 at 7:14 PM Luigi Faino ***@***.***>
> wrote:
>
>> @ncgrjsmiao <https://github.com/ncgrjsmiao> you can keep the AAT
>> folder, but i would suggest to clean all.
>>
>> Cheers
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <#16 (comment)>, or mute
>> the thread
>> <https://github.com/notifications/unsubscribe-auth/ADSIDOEZJYPEUUPRQIF4YNDPSA6ILANCNFSM4HBO2ZRQ>
>> .
>>
>
|
@zcrself |
No, NameError! I do not know what is the reason? How to solve it?
[image: amazon_ec2_evm_error.PNG]
…On Tue, Apr 30, 2019 at 8:03 PM Luigi Faino ***@***.***> wrote:
@zcrself <https://github.com/zcrself>
did it finish?
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|
I test the example dataset within singularity, but met some probelm until ###GMAP MAPPING STARTED AT: 13:06:26 21-03 ###
###BUILD INDEX###
bellow is Error message:
Traceback (most recent call last):
File "/opt/LoReAn/code/lorean.py", line 552, in
main()
File "/opt/LoReAn/code/lorean.py", line 497, in main
args.verbose, Fflag=True)
File "/opt/LoReAn/code/mapping.py", line 398, in gmap
wd, Fflag, type_out, verbose)
File "/opt/LoReAn/code/mapping.py", line 130, in gmap_map
filename = longest_cds(list_fasta[0][1], list_fasta[1][1], verbose, working_dir, filename)
File "/opt/LoReAn/code/mapping.py", line 188, in longest_cds
db = gffutils.create_db(gff_file, ':memory:', merge_strategy='create_unique', keep_order=True, transform=transform)
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 1288, in create_db
c.create()
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 504, in create
self._populate_from_lines(self.iterator)
File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 625, in _populate_from_lines
raise ValueError("No lines parsed -- was an empty file provided?")
ValueError: No lines parsed -- was an empty file provided?
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