Error for ieu-b-2

[Sarah Gagliano Taliun]

Hello,

Thanks for creating this tool. We've been exploring BIGA and noticed that specifying the following study ID ieu-b-2 from the IEU Open GWAS project for an LDSC job results in an error. This dataset has already been harmonized by BIGA, and ieu-b-2.vcf.gz is successfully saved according to the log, but the next part, "Starting to map rsid to chromosome and position", results in the following error: 

Traceback (most recent call last):
  File "/home/django/bigagwas/queueTasks/tasks/tasks.py", line 437, in gene_corr_run
    job_settings = process_universal_input(job_settings)
  File "/home/django/bigagwas/queueTasks/tasks/tasks_process_input.py", line 596, in process_universal_input
    job_settings = map_rsid(job_settings, log)
  File "/home/django/bigagwas/queueTasks/tasks/tasks_process_input.py", line 187, in map_rsid
    p.map(single_map_snp, args)
  File "/root/anaconda3/envs/brimge/lib/python3.8/site-packages/billiard/pool.py", line 1416, in map
    return self.map_async(func, iterable, chunksize).get()
  File "/root/anaconda3/envs/brimge/lib/python3.8/site-packages/billiard/pool.py", line 1791, in get
    raise self._value.exception
KeyError: ['eaf']

We've experimented with a few other IDs from the IEU OpenGWAS project, and they run fine.

Thank you! 

[yujue23]

Thank you for using BIGA and bringing this to our attention.

Based on the log output, this job indeed did not pass our harmonization. Briefly, the “ieu-b-2.vcf.gz” was successfully downloaded from IEU Open GWAS. However, this dataset does not contain the allele frequency column (“eaf”), which is required by our harmonization. Therefore, the job is stopped due to data missingness. (it says "Starting to map rsid to chromosome and position," because this is supposed to be the next harmonization step…)

Recently we have noticed that our log system especially the input data error message may not be very clear. So we are actually planning to update our log system this weekend! We will keep you posted once the updates are completed.

Thanks a lot again and just let us know if you have any suggestions to improve BIGA!

Best,

Yujue