root - ERROR - Killing request for url

[raonyguimaraes]

I am getting this error when trying to run postgap for 100 variants:

python POSTGAP.py --summary_stat input.tsv --database_dir databases/
08/06/2020 12:38:05 PM - root - ERROR - Killing request for url: http://rest.ensembl.org/eqtl/variant_name/homo_sapiens/rs7523364?content-type=application/json;statistic=p-value

URL opens just fine in the browser.

[dzerbino]

Hello @raonyguimaraes ,

That's curious, could you please send me the entire log?

Thank you,

Daniel

[raonyguimaraes]

Here is the full log file: postgap.log

It's mostly complaining about the LD matrix: 08/06/2020 05:03:46 PM - root - ERROR - LD matrix is identity matrix!

This error is probably because my ulimit values were too low, so let me increase that and run it again!

Traceback (most recent call last):
File "POSTGAP.py", line 690, in
main()
File "POSTGAP.py", line 153, in main
formatted_results = pretty_output(res, options.population)
File "POSTGAP.py", line 435, in pretty_output
content = filter(lambda X: len(X) > 0, [pretty_cluster_association(association, population) for association in
associations])
File "POSTGAP.py", line 447, in pretty_cluster_association
results = genecluster_association_table(association, population)
File "POSTGAP.py", line 466, in genecluster_association_table
ld_snp_ids, r_matrix = postgap.LD.get_pairwise_ld(association.cluster.ld_snps, population)
File "REDACTED*/postgap/lib/postgap/LD.py", line 241, in get_pairwise_ld
process = Popen(ld_comm, stdout=PIPE, stderr=PIPE)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 928, in _execute_child
errpipe_read, errpipe_write = self.pipe_cloexec()
File "/usr/lib/python2.7/subprocess.py", line 865, in pipe_cloexec
r, w = os.pipe()
OSError: [Errno 24] Too many open files

real 190m44.836s
user 24m45.199s
sys 11m58.285s

[dzerbino]

OK let me know.

Cheers,

Daniel