search

shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
56 stars 12 forks source link

missing python package #34

Closed mihinduk closed 3 years ago

mihinduk commented 3 years ago

When I run the test data, it dies with this error:

Error executing rule sankey_diagram on cluster (jobid: 213, external: Submitted batch job 33397859, jobscript: /scratch/sahlab/RC2_IBD_virome/te st/.snakemake/tmp.1edmh2g2/snakejob.sankey_diagram.213.sh). For error details see the cluster log and the log files of the involved rule(s). Job failed, going on with independent jobs. [Thu Oct 28 01:20:39 2021] Finished job 196. 214 of 216 steps (99%) done Exiting because a job execution failed. Look above for error message Complete log: /scratch/sahlab/RC2_IBD_virome/test/.snakemake/log/2021-10-27T220225.813094.snakemake.log ERROR: Snakemake command failed

ERROR:snakemake.logging:RuleException: ValueError in line 501 of /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/snakemake/workflow/rules/04_summaries.smk:

Image export using the "kaleido" engine requires the kaleido package, which can be installed using pip: $ pip install -U kaleido

File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 2357, in run _wrapper File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/snakemake/workflow/rules/04_summaries.smk", line 501, in rule_sankey_diagram File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/basedatatypes.py", line 3821, in write_image File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/io/_kaleido.py", line 268, in write_image File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/io/_kaleido.py", line 134, in to_image File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 574, in _cal lback File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/concurrent/futures/thread.py", line 52, in run File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 560, in cach ed_or_run File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init__.py", line 2390, in run _wrapper

beardymcjohnface commented 3 years ago

Fix is in dev and will be in the next build.