Closed marrip closed 6 months ago
This is fixed in the updated script.
Hello @xiaoliz0 , i see you closed this issue and mentioned that it is fixed in the updated script. We are using v1.2.0 and still facing the same error...
Traceback (most recent call last):
File "/pronto/Script/PRONTO.py", line 1337, in <module>
main(sys.argv[1:])
File "/pronto/Script/PRONTO.py", line 1108, in main
all_data_config_DepthTumor_DNA = filter_depth_tumor_all_col(all_data,filter1_min_depth_tumor_DNA)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/pronto/Script/PRONTO.py", line 189, in filter_depth_tumor_all_col
data.append(data_config[0])
~~~~~~~~~~~^^^
IndexError: list index out of range
Can you please look into this? Thank you
Hello, Yes, this is fixed in the branch develop_OUS. I will create a push request and you could check the overview.
We had a problem with an empty variant table today. We had a sample with a small amount of reads and were not aware of it (got LocalApp results with only 2 variants which were filtered out leaving no variants in the small variants table). When we ran PRONTO, we just got this error message:
I would opt for checking that the file actually contains something before trying to give it to
filter_depth_tumor_all_col()
which then fails. The error message should state the file path and maybe sample id.