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problems in setup process #53

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ningyuanlu opened this issue Jul 3, 2024 · 0 comments
Open

problems in setup process #53

ningyuanlu opened this issue Jul 3, 2024 · 0 comments

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@ningyuanlu
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When I process mantis setup, only NOG is downloaded.
The main packages I use are:
Python v3.7.3
requests v2.22.0
numpy v1.18.1
nltk v3.4.4
psutil 5.6.7
[HMMER] v3.2.1
GCC
Errors comes as below:
(mantis) [luningyuan@localhost ~]$ mantis setup
Executing command:
/data/home/luningyuan/anaconda3/envs/mantis/bin/mantis setup

Setting up databases

Default references folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/
Custom references folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/Custom_references/
TAX NOG references folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/
TAX NCBI references folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NCBI/
Pfam reference folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/pfam/
KOfam reference folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/kofam/
TCDB reference folder:
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/tcdb/
------------------------------------------# Weights:
nog:0.8, pfam:0.9

Will check data for the following NOGT:
5139,1511857,45401,135613,69541,119065,586,995019,34383,265,10656,1357,84406,213115,285107,5148,245186,32199,35718,5794,225057,1060,5338,85013,1283313,6231,28890,118969,629,5819,29000,267894,97050,766,28883,363408,1164882,1303,53433,35278,119045,506,85012,203691,52604,200930,92860,10744,110618,1236,76804,675063,147541,31979,183925,547,135625,1016,1239,1189,2759,335928,75682,191028,1386,33342,145357,541000,766764,117747,206389,59732,28037,1506553,4447,69277,74030,8459,7088,186824,150247,204037,2063,909932,118884,32066,1268,85016,508458,5129,558415,1150,256005,35268,203682,10841,68892,122277,200918,622450,539002,265975,237,671232,28216,40674,28211,91835,1762,10662,85021,561,35493,186820,6236,7742,58840,85018,93682,590,74385,186813,84992,9989,639021,186827,135619,189775,183967,82986,186806,4776,29547,186823,267893,267890,1212,200795,135614,201174,34397,32061,400634,147548,204428,52018,613,538999,32003,7148,46205,326319,80864,5796,157897,85019,34037,85020,119043,451866,119069,200940,183963,213113,6656,84995,10239,104264,186822,33554,57723,1142,53335,171550,136846,33090,216572,119089,186804,5809,5863,1653,61432,33183,91561,50557,976,423358,155619,189330,5042,244698,81850,7147,147550,85025,186928,289201,91061,136841,651137,213462,38820,204432,2836,135623,35237,85009,119603,83612,167375,200643,1100069,136843,314294,10699,629295,815,186818,129337,29258,182709,81852,10860,11632,33213,5234,5653,11157,183980,85004,4891,11989,326457,526524,713636,85026,31993,85010,135618,9263,768503,10404,72273,39782,4890,112252,5878,7399,82117,451870,468,186807,283735,308865,7711,183939,213481,1224,118882,35301,548681,60136,439488,302485,290174,1161,252356,119060,33867,29,33958,1028384,68295,85017,583,135624,224756,1305,7898,464095,85023,28221,5151,72275,228398,554915,9604,1129,82115,178469,186821,52959,85014,255475,41294,830,204457,206350,1,1313,311790,69657,204458,203494,34008,355688,34384,3699,28889,1297,9443,136845,2433,1307,74201,252301,171551,186801,2,267889,213118,45404,544448,5204,68525,2323,43988,8782,3041,414999,147545,142182,314146,85005,136849,84998,422676,267888,121069,4893,544,572511,1570339,10477,68298,206351,117743,5125,7214,33154,183968,246874,186828,1090,119066,551,10474,9397,452284,200783,71274,358033,45667,2157,4751,191675,33208,85008,90964,204441,40117,10,76831,35325,1117,301297,772,451867
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/eggnog.db.gz
Downloading from http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz. The file will be kept in /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/
Gunzipping /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/eggnog.db.gz to /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/eggnog.db
/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/Pfam-A.hmm.dat.gz
Downloading from http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz. The file will be kept in /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/
Gunzipping /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/Pfam-A.hmm.dat.gz to /data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/References/NOG/Pfam-A.hmm.dat
Database will be setup with 7 workers!
Process Process-2:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-3:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-4:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-5:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-6:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-8:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Process Process-7:
Traceback (most recent call last):
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/data/home/luningyuan/anaconda3/envs/mantis/lib/python3.7/site-packages/mantis/Database_generator.py", line 194, in worker_setup_databases
database, taxon_id, stdout_path = record
ValueError: not enough values to unpack (expected 3, got 2)
Ran into an issue, check the log for details. Exitting!

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