kevinkle
commented
5 years ago kevin@panther ~/prairiedog> snakemake -j 8
Building DAG of jobs...
2019-07-04 14:21:01 panther snakemake.logging[6900] WARNING Building DAG of jobs...
Using shell: /bin/bash
2019-07-04 14:21:01 panther snakemake.logging[6900] WARNING Using shell: /bin/bash
Provided cores: 8
2019-07-04 14:21:01 panther snakemake.logging[6900] WARNING Provided cores: 8
Rules claiming more threads will be scaled down.
2019-07-04 14:21:01 panther snakemake.logging[6900] WARNING Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 done
40 pangenome
1 preload
43
2019-07-04 14:21:01 panther snakemake.logging[6900] WARNING Job counts:
count jobs
1 all
1 done
40 pangenome
1 preload
43
2019-07-04 14:21:01 panther snakemake.logging[6900] INFO
[Thu Jul 4 14:21:01 2019]
2019-07-04 14:21:01 panther snakemake.logging[6900] INFO [Thu Jul 4 14:21:01 2019]
rule preload:
output: outputs/preloaded.txt
jobid: 43
2019-07-04 14:21:01 panther snakemake.logging[6900] INFO rule preload:
output: outputs/preloaded.txt
jobid: 43
2019-07-04 14:21:01 panther snakemake.logging[6900] INFO
Job counts:
count jobs
1 preload
1
2019-07-04 14:21:02 panther snakemake.logging[6969] WARNING Job counts:
count jobs
1 preload
1
2019-07-04 14:21:02 panther prairiedog[6969] DEBUG Done initializing Dgraph client
[Thu Jul 4 14:21:02 2019]
2019-07-04 14:21:02 panther snakemake.logging[6969] INFO [Thu Jul 4 14:21:02 2019]
Error in rule preload:
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR Error in rule preload:
jobid: 0
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR jobid: 0
output: outputs/preloaded.txt
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR output: outputs/preloaded.txt
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR
RuleException:
_Rendezvous in line 54 of /home/kevin/prairiedog/Snakefile:
<_Rendezvous of RPC that terminated with:
status = StatusCode.RESOURCE_EXHAUSTED
details = "received trailing metadata size exceeds limit"
debug_error_string = "{"created":"@1562271662.608099591","description":"Error received from peer ipv6:[::1]:9080","file":"src/core/lib/surface/call.cc","file_line":1052,"grpc_message":"received trailing metadata size exceeds limit","grpc_status":8}"
>
File "/home/kevin/prairiedog/Snakefile", line 54, in __rule_preload
File "/home/kevin/prairiedog/prairiedog/dgraph.py", line 43, in preload
File "/home/kevin/prairiedog/prairiedog/dgraph.py", line 73, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 141, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 188, in _common_except_mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 119, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/client_stub.py", line 56, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/grpc/_channel.py", line 565, in __call__
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/grpc/_channel.py", line 467, in _end_unary_response_blocking
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/concurrent/futures/thread.py", line 57, in run
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR RuleException:
_Rendezvous in line 54 of /home/kevin/prairiedog/Snakefile:
<_Rendezvous of RPC that terminated with:
status = StatusCode.RESOURCE_EXHAUSTED
details = "received trailing metadata size exceeds limit"
debug_error_string = "{"created":"@1562271662.608099591","description":"Error received from peer ipv6:[::1]:9080","file":"src/core/lib/surface/call.cc","file_line":1052,"grpc_message":"received trailing metadata size exceeds limit","grpc_status":8}"
>
File "/home/kevin/prairiedog/Snakefile", line 54, in __rule_preload
File "/home/kevin/prairiedog/prairiedog/dgraph.py", line 43, in preload
File "/home/kevin/prairiedog/prairiedog/dgraph.py", line 73, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 141, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 188, in _common_except_mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/txn.py", line 119, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pydgraph/client_stub.py", line 56, in mutate
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/grpc/_channel.py", line 565, in __call__
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/site-packages/grpc/_channel.py", line 467, in _end_unary_response_blocking
File "/home/kevin/.pyenv/versions/3.7.3/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message
2019-07-04 14:21:02 panther snakemake.logging[6969] ERROR Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
2019-07-04 14:21:02 panther snakemake.logging[6900] WARNING Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
2019-07-04 14:21:02 panther snakemake.logging[6900] ERROR Exiting because a job execution failed. Look above for error message
Complete log: /home/kevin/prairiedog/.snakemake/log/2019-07-04T142100.494377.snakemake.log
2019-07-04 14:21:02 panther snakemake.logging[6900] WARNING Complete log: /home/kevin/prairiedog/.snakemake/log/2019-07-04T142100.494377.snakemake.log
When preloading per #105