Error executing rule get_vep_cache on cluster

[snakemake]

Error executing rule get_vep_cache on cluster

[moldach]

Forgot to include the contents of nohup.out and cache.log so here they here after re-submitting with the -rparam:

nohup.out

Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 1
Job counts:
        count   jobs
        1       all
        1       get_vep_cache
        2
Welcome to the CBC MILP Solver 
Version: 2.9.0 
Build Date: Feb 12 2015 

command line - /home/moldach/miniconda3/envs/python3.8.5/lib/python3.8/site-packages/pulp/apis/../solverdir/cbc/linux/64/cbc /tmp/284a632f5b474619aeca12ff1c05d1c8-pulp.mps max ratio None allow None threa
ds None presolve on strong None gomory on knapsack on probing on branch printingOptions all solution /tmp/284a632f5b474619aeca12ff1c05d1c8-pulp.sol (default strategy 1)
At line 2 NAME          MODEL
At line 3 ROWS
At line 7 COLUMNS
At line 13 RHS
At line 16 BOUNDS
At line 18 ENDATA
Problem MODEL has 2 rows, 1 columns and 2 elements
Coin0008I MODEL read with 0 errors
String of None is illegal for double parameter ratioGap value remains 0
String of None is illegal for double parameter allowableGap value remains 0
String of None is illegal for integer parameter threads value remains 0
String of None is illegal for integer parameter strongBranching value remains 5
Option for gomoryCuts changed from ifmove to on
Option for knapsackCuts changed from ifmove to on
Continuous objective value is 2 - 0.00 seconds
Cgl0004I processed model has 0 rows, 0 columns (0 integer (0 of which binary)) and 0 elements
Cbc3007W No integer variables - nothing to do
Cuts at root node changed objective from -2 to -1.79769e+308
Probing was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Gomory was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Knapsack was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Clique was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
MixedIntegerRounding2 was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
FlowCover was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
TwoMirCuts was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)

Result - Optimal solution found

Objective value:                2.00000000
Enumerated nodes:               0
Total iterations:               0
Time (CPU seconds):             0.00
Time (Wallclock seconds):       0.00

Option for printingOptions changed from normal to all
Total time (CPU seconds):       0.00   (Wallclock seconds):       0.00

/home/moldach/miniconda3/envs/python3.8.5/lib/python3.8/site-packages/pulp/pulp.py:1195: UserWarning: Spaces are not permitted in the name. Converted to '_'
  warnings.warn("Spaces are not permitted in the name. Converted to '_'")

[Thu Aug 27 16:41:34 2020]
rule get_vep_cache:
    output: resources/vep/cache
    log: logs/vep/cache.log
    jobid: 1
    reason: Missing output files: resources/vep/cache

Submitted job 1 with external jobid '89369 logs/cluster/get_vep_cache/unique/jobid1_b4ae59b8-6b06-4e9c-9dfa-e0285b6fc96a.out'.
[Thu Aug 27 16:41:54 2020]
Error in rule get_vep_cache:
    jobid: 1
    output: resources/vep/cache
    log: logs/vep/cache.log (check log file(s) for error message)
    conda-env: /gpfs/home/moldach/projects/saliva/SIMPLE_TEST/.snakemake/conda/60d0d409
    cluster_jobid: 89369 logs/cluster/get_vep_cache/unique/jobid1_b4ae59b8-6b06-4e9c-9dfa-e0285b6fc96a.out

Error executing rule get_vep_cache on cluster (jobid: 1, external: 89369 logs/cluster/get_vep_cache/unique/jobid1_b4ae59b8-6b06-4e9c-9dfa-e0285b6fc96a.out, jobscript: /gpfs/home/moldach/projects/saliva/SIMPLE_TEST/.snakemake/tmp.jp12ytjb/snakejob.get_vep_cache.1.sh). For error details see the cluster log and the log files of the involved rule(s).
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /gpfs/home/moldach/projects/saliva/SIMPLE_TEST/.snakemake/log/2020-08-27T164133.682942.snakemake.log

cache.log

perl: symbol lookup error: /home/moldach/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck

[mbhall88]

Is this a cross-post of snakemake/snakemake#586 effectively?

[moldach]

Effectively yes - I was trying this on another software architecture - however, it appears the problem was #586