rvalieris
commented
1 year ago hello, looks like either the markers on the pools data could have some missing values or zero values that resulted in this error, can you check the outputs/variants_table/pango-markers-table.tsv and outputs/variants_table/pool_samples_mypool.tsv files and make sure the data looks good ? alternatively if possible, can you send me the files I can check this.
(lcs) test@NCIM-Workstation2:/data/Student_Data/LCS-master$ snakemake --config markers=pango dataset=mypool --cores 70 --resources mem_gb=200 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 70 Rules claiming more threads will be scaled down. Provided resources: mem_gb=200 Job stats: job count min threads max threads
all 1 1 1 decompose 1 50 50 total 2 1 50
Select jobs to execute...
[Wed Nov 30 19:15:17 2022] rule decompose: input: outputs/variants_table/pango-markers-table.tsv, outputs/variants_table/pool_samples_mypool.tsv output: outputs/decompose/mypool.status, outputs/decompose/mypool.out jobid: 1 reason: Missing output files: outputs/decompose/mypool.out threads: 50 resources: tmpdir=/tmp, mem_gb=160
using 285 markers to estimate 22 variant groups (solve pid=1333588) WARNING - large complementary slackness residual: 0.025679 (solve pid=1334345) WARNING - large complementary slackness residual: 0.033062 Traceback (most recent call last): File "/data/Student_Data/Vinay/LCS-master/scripts/vg-decompose.py", line 185, in
main()
File "/data/Student_Data/Vinay/LCS-master/scripts/vg-decompose.py", line 182, in main
solve_samples(markers_df, pools, marker_snps_list, tags, pool_tags)
File "/data/Student_Data/Vinay/LCS-master/scripts/vg-decompose.py", line 129, in solve_samples
prob, result, x = ray.get(wid)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/ray/_private/client_mode_hook.py", line 105, in wrapper
return func(*args, **kwargs)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/ray/worker.py", line 1809, in get
raise value.as_instanceof_cause()
ray.exceptions.RayTaskError(ValueError): ray::solve() (pid=1341823, ip=172.28.28.88)
File "/data/Student_Data/Vinay/LCS-master/scripts/vg-decompose.py", line 45, in solve
objective = cvxpy.Minimize(negLLH(x, vs, ps_m, ps_dp - ps_m))
File "/data/Student_Data/Vinay/LCS-master/scripts/vg-decompose.py", line 33, in negLLH
ps = cvxpy.matmul(vars_snps, f)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/atoms/affine/binary_operators.py", line 86, in matmul
return MulExpression(lh_exp, rh_exp)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/atoms/affine/binary_operators.py", line 50, in init
super(BinaryOperator, self).init(lh_exp, rh_exp)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/atoms/atom.py", line 49, in init
self.args = [Atom.cast_to_const(arg) for arg in args]
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/atoms/atom.py", line 49, in
self.args = [Atom.cast_to_const(arg) for arg in args]
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/expressions/expression.py", line 507, in cast_to_const
return expr if isinstance(expr, Expression) else cvxtypes.constant()(expr)
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/expressions/constants/constant.py", line 58, in init
super(Constant, self).init(intf.shape(self.value))
File "/home/test/anaconda3/envs/lcs/lib/python3.9/site-packages/cvxpy/expressions/leaf.py", line 108, in init
raise ValueError("Invalid dimensions %s." % (shape,))
ValueError: Invalid dimensions (0, 22).
[Wed Nov 30 19:18:09 2022]
Error in rule decompose:
jobid: 1
output: outputs/decompose/mypool.status, outputs/decompose/mypool.out
shell:
python scripts/vg-decompose.py -m outputs/variants_table/pango-markers-table.tsv -p outputs/variants_table/pool_samples_mypool.tsv -o outputs/decompose/mypool.out -s outputs/decompose/mypool.status --threads 50
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job decompose since they might be corrupted: outputs/decompose/mypool.status, outputs/decompose/mypool.out Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2022-11-30T191514.901726.snakemake.log (lcs) test@NCIM-Workstation2:/data/Student_Data/Vinay/LCS-master$