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konradjk / loftee

MIT License
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Failed to instantiate plugin LoF #24

Open Melb1 opened 7 years ago

Melb1 commented 7 years ago

Hi Daniel

i am running Loftee and getting these two error.

  1. Use of uninitialized value in string eq at /home/ubuntu/.vep/Plugins/LoF.pm line 309.
  2. WARNING: Failed to instantiate plugin LoF: Can't open /humgen/atgu1/fs03/birnbaum/loftee-dev/splice_data/donor_motifs/ese.txt: No such file or directory at /home/ubuntu/.vep/Plugins/loftee_splice_utils.pl line 210
birndle commented 7 years ago

Hello -

I believe both issues will be fixed if you specify the path to your loftee directory when you run VEP; i.e. perl variant_effect_predictor.pl [--other options to VEP] --plugin LoF,loftee_path:/path/to/loftee,[other options to loftee]

This will tell VEP to look in this directory for the files splice_data/donor_motifs/*. Note that this means the "splice_data" directory (and its contents) shared in the loftee repo must be found at that loftee_path. Hope this helps.

Melb1 commented 7 years ago

Hi Dan

Thanks very much. I really appreciate your correspondence It worked perfectly

Now i am getting this warning !:

Use of uninitialized value $faidx in split at /home/ubuntu/.vep/Plugins/LoF.pm line 492, <__ANONIO__> line 5064.

I have samtools v1.3 and .gz files for reference genome fatsa and index.

Your response will be appreciated?

Regards Moeen Riaz

On 9 November 2017 at 04:57, Daniel Birnbaum notifications@github.com wrote:

Hello -

I believe both issues will be fixed if you specify the path to your loftee directory when you run VEP; i.e. perl variant_effect_predictor.pl [--other options to VEP] --plugin LoF,loftee_path:/path/to/loftee,[other options to loftee]

This will tell VEP to look in this directory for the files splice_data/donor_motifs/*. Note that this means the "splice_data" directory (and its contents) shared in the loftee repo must be found at that loftee_path. Hope this helps.

  • Dan

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claudiadast commented 6 years ago

I am also experiencing a similar issue as @Melb1 above (after resolving the same first issue). It says:

WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) at /home/ec2-user/.vep/Plugins/gerp_dist.pl line 129, <__ANONIO__> line 53522.
hliang commented 6 years ago

@claudiadast I got similar error. After setting conservation_file, that issue is gone. Although another error popped up for me (might related to gerp_file)

nunonog commented 5 years ago

I am also experiencing a similar issue as @Melb1 above (after resolving the same first issue). It says:

WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) at /home/ec2-user/.vep/Plugins/gerp_dist.pl line 129, <__ANONIO__> line 53522.

Hi, I know this is year old, but I am experiencing the exact same issue as @claudiadast (copied above) Any solution to this?

Thanks in advance

Frogdong commented 3 years ago

I am also experiencing a similar issue as @Melb1 above (after resolving the same first issue). It says:

WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) at /home/ec2-user/.vep/Plugins/gerp_dist.pl line 129, <__ANONIO__> line 53522.

Hi, I know this is year old, but I am experiencing the exact same issue as @claudiadast (copied above) Any solution to this?

Thanks in advance

May I ask did you solve this problem? Many thanks!

nunonog commented 3 years ago

Hi @Frogdong , I don't think I did (it has been some time now...), I ended up continuing with another alternative. I will perhaps look at it again soon, and I can get back to you with my notes.

Are having the same issue?

Frogdong commented 3 years ago

Hi @Frogdong , I don't think I did (it has been some time now...), I ended up continuing with another alternative. I will perhaps look at it again soon, and I can get back to you with my notes.

Are having the same issue?

Hi @nunonog , Yes, I am experiencing the same issue. And even after setting conservation_file, it still happens. It will be great that if you can share your notes. BTW, could you share the alternative? Thanks again.