index out of range error

kleigeb commented 6 years ago

Getting the following error when trying to run SISRS with the test data provided:

748768 total variable sites (alignment.nex)
Traceback (most recent call last):
  File "/software/SISRS-1.6.2/libexec/sisrs/get_alignment_Memory.py", line 243, in <module>
    numbi=alignment.numsnps()
  File "/software/SISRS-1.6.2/libexec/sisrs/get_alignment_Memory.py", line 40, in numsnps
    if c[1][1]==1:
IndexError: list index out of range
get_alignment.py failed

I ran the following command from the test data directory to produce the command:

$ /software/SISRS-1.6.2/bin/sisrs sites -g 1745690 -p 24

Let me know if there's any more info I can provide to help find a resolution. Thanks.

BobLiterman commented 6 years ago

To clarify so that I can try to replicate, you're using the test data from here?

https://github.com/rachelss/SISRS_test_data

kleigeb commented 6 years ago

Correct.

On Tue, Mar 20, 2018 at 4:41 PM, Bob Literman notifications@github.com wrote:

To clarify so that I can try to replicate, you're using the test data from here?

https://github.com/rachelss/SISRS_test_data

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rachelss/SISRS/issues/59#issuecomment-374766555, or mute the thread https://github.com/notifications/unsubscribe-auth/AXZaKwetg3zCA8tdpLoK2OgI-TJ4IsOoks5tgXd4gaJpZM4SyrwW .

BobLiterman commented 6 years ago

Alright, dove into the code and found what could have been the offending line. I was able to replicate your error, and then remove it. Clone the new code from GitHub and give it a shot?

Thanks for the heads up!

kleigeb commented 6 years ago

Thanks! I'll give it a shot tomorrow morning and get back to you.

On Tue, Mar 20, 2018, 6:16 PM Bob Literman notifications@github.com wrote:

Alright, dove into the code and found what could have been the offending line. I was able to replicate your error, and then remove it. Clone the new code from GitHub and give it a shot?

Thanks for the heads up!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rachelss/SISRS/issues/59#issuecomment-374789471, or mute the thread https://github.com/notifications/unsubscribe-auth/AXZaKxgzFb5BjJeOtzytKCelVLOUtYptks5tgY26gaJpZM4SyrwW .

kleigeb commented 6 years ago

Ran with the test data this morning and everything completed successfully! Thanks for your lightning fast help!

On Tue, Mar 20, 2018 at 6:39 PM, Kevin Leigeb kevin.leigeb@gmail.com wrote:

Thanks! I'll give it a shot tomorrow morning and get back to you.

On Tue, Mar 20, 2018, 6:16 PM Bob Literman notifications@github.com wrote:

Alright, dove into the code and found what could have been the offending line. I was able to replicate your error, and then remove it. Clone the new code from GitHub and give it a shot?

Thanks for the heads up!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rachelss/SISRS/issues/59#issuecomment-374789471, or mute the thread https://github.com/notifications/unsubscribe-auth/AXZaKxgzFb5BjJeOtzytKCelVLOUtYptks5tgY26gaJpZM4SyrwW .

rachelss / SISRS

index out of range error #59