getting crashed

[Vikash84]

Making lineages: 7%|██▍ | 20724/277641 [00:14<02:51, 1497.39 taxids/s]multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/vsingh/.conda/envs/tango/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/assign.py", line 490, in process_lineages
x = add_names(x, taxid, ncbi_taxa)
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/assign.py", line 114, in add_names
if t < 0:
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/pandas/core/generic.py", line 1576, in nonzero
.format(self.class.name))
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/vsingh/.conda/envs/tango/bin/tango", line 12, in
sys.exit(main())
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/main.py", line 283, in main
args.func(args)
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/main.py", line 77, in assign_taxonomy
args.rank_thresholds, args.taxdir, args.sqlitedb, args.chunksize, args.cpus)
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/assign.py", line 776, in parse_hits
lineage_df, name_dict = make_lineage_df(taxids, taxdir, sqlitedb, reportranks, cpus)
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tango/assign.py", line 561, in make_lineage_df
unit=" taxids", ncols=100))
File "/home/vsingh/.conda/envs/tango/lib/python3.5/site-packages/tqdm/std.py", line 1093, in iter
for obj in iterable:
File "/home/vsingh/.conda/envs/tango/lib/python3.5/multiprocessing/pool.py", line 731, in next
raise value
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

[johnne]

Hi @Vikash84,
Sorry about not getting back to you earlier.

What version of tango were you using for this? Is it possible for you to upload some parts of the input used that caused this error?

[Vikash84]

I have observed when data size is small it work s fine, but for large data size it generally get crashed.

At that time i was using tango 0.5.7.

[johnne]

From the error message I get a sense it may be related to missing and/or duplicate taxid entries in some way. What database did you use when this happened? Could you try with the latest version? (Please note that the package has changed name to contigtax)

[Vikash84]

I was using NCBI nr database. Sure I will give a try with latest version i.e contigtax.

[johnne]

Thanks! Let me know how it goes.