GFF3 error

[Juliana Chu]

Hello, there!

I'm trying to use majiq for arabidopsis thaliana, and for the gff3 file, I downloaded from TAIR10. However, when I tried to run the command, it gave me an error saying "ValueError: not enough values to unpack (expected 2, got 1)". I found that the gff3 files I downloaded from TAIR mostly have only one phrase. Then, I wonder, does this error message means that we need at least two phrases to make MAJIQ work? Then, if that is the case, can arabidopsis thaliana be ran by MAJIQ. If yes, then where can I get the gff3 file, or how can I convert it? 

This is an example I've got from TAIR:

This is the error message I've got:

2021-01-06 22:32:18,639 (PID:5889) - INFO - Parsing GFF3

Traceback (most recent call last):

  File "/Users/ju.chu/env/bin/majiq", line 11, in <module>

    load_entry_point('majiq==2.2', 'console_scripts', 'majiq')()

  File "/Users/ju.chu/env/lib/python3.8/site-packages/majiq/run_majiq.py", line 529, in main

    args.func(args)

  File "majiq/src/build.pyx", line 659, in majiq.src.build.build

  File "/Users/ju.chu/env/lib/python3.8/site-packages/majiq/src/basic_pipeline.py", line 13, in pipeline_run

    return pipeline.run()

  File "majiq/src/build.pyx", line 669, in majiq.src.build.Builder.run

  File "majiq/src/build.pyx", line 677, in majiq.src.build.Builder.builder

  File "majiq/src/build.pyx", line 580, in majiq.src.build._core_build

  File "majiq/src/io.pyx", line 52, in majiq.src.io.read_gff

  File "/Users/ju.chu/env/lib/python3.8/site-packages/majiq/src/gff.py", line 74, in parse_gff3

    "attributes": __parse_gff_attributes(parts[8]),

  File "/Users/ju.chu/env/lib/python3.8/site-packages/majiq/src/gff.py", line 34, in __parse_gff_attributes

    key, value = attribute.split("=")

ValueError: not enough values to unpack (expected 2, got 1)

THANK YOU !

[Paul Jewell]

Good Afternoon, 

This is indeed based on a format of the gff standard we had not used / encountered before. One of our contributors, Joseph, has created a small change which should serve in your case as a workaround for this issue. We would be interested to hear your feedback on the fix. 

Can you please use the following steps to try the patched version?

$ git clone <the academic majiq repository link>

$ git checkout fix-trailing-semicolons-gff3

$ pip install ./majiq 

(should be done in a virtualenv or other environmentwrapper that you use)

Let us know if this resolves the issue!

Thanks, 

-Paul

[Juliana Chu]

Hello, sorry for late reply

For the comment :$ git clone <the academic majiq repository link>, I entered the link without the git+ at the beginning, and it returns for an error, saying the repository is not found. The repository I used is from the email I got after registering on Majiq, and it gives me a git link which is from biocipher. I wonder am I using the correct link?

Thanks,

Juliana 

[Paul Jewell]

Hello Juliana, 

You also need to remove the "#egg=majiq" from the end, so that it goes like $ git clone https:// <rest of url> .git

Let me know if that works. 

Thanks, 

-Paul

[Juliana Chu]

Hello, Paul!

I have succeed the first part, but when I type in command :git checkout fix-trailing-semicolons-gff3

it gives me an error saying :

error: pathspec 'fix-trailing-semicolons-gff3' did not match any file(s) known to git

I don't know what is wrong with the command, since from the first command, it was all done.

Thanks,

-Juliana 

[Paul Jewell]

Hi Juliana, 

Could you please try instead:

$ git checkout origin/fix-trailing-semicolons-gff3

?

Let me know if that produces a different message. 

Thanks, 

-Paul

[Joseph Aicher]

Dear Juliana,

To add to that, don't forget to pull updates from bitbucket before running the checkout command (i.e. run `git pull` before running `git checkout fix...`)

Best,

Joseph

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[Juliana Chu]

Hello Joseph and Paul,

Thank you for the advice. I have used the git pull <url>, and ran the command 'git checkout...', it gave me the same error message as before.         

error: pathspec 'origin/fix-trailing-semicolons-gff3' did not match any file(s) known to git

This is the message after I ran git pull:

remote: Counting objects: 23936, done.

remote: Compressing objects: 100% (5761/5761), done.

remote: Total 23936 (delta 18125), reused 23894 (delta 18097)

Receiving objects: 100% (23936/23936), 21.37 MiB | 536.00 KiB/s, done.

Resolving deltas: 100% (18125/18125), done.

From https://bitbucket.org/biociphers/majiq_academic

 * branch            HEAD       -> FETCH_HEAD

Thanks,

Juliana 

[Paul Jewell]

Hi Juliana, 

I've ran these exact commands in a new, blank directory:

$ git clone https://bitbucket.org/biociphers/majiq_academic

$ cd majiq_academic/

$ git checkout origin/fix-trailing-semicolons-gff3

Following this, the only warning I See is about being in a 'detached HEAD' state, which is fine and may be ignored. 

Can you please let me know which OS you are using, and which version of `git` is installed? It seems like something strange is amiss on your system. Could you also please show the above three commands and their output on your system, just so I can see if I might have missed anything?

Thank you, 

-Paul