karel-brinda
commented
5 years ago Could you please upload your Snakefile and coverage.txt? It would also be useful to see your ref.fa.fai (can be obtained by samtools faidx ref.fa).
Open zihhuafang opened 5 years ago
karel-brinda
commented
5 years ago Could you please upload your Snakefile and coverage.txt? It would also be useful to see your ref.fa.fai (can be obtained by samtools faidx ref.fa).
zihhuafang
commented
5 years ago I put all the files here: https://www.dropbox.com/sh/455d8m45vqderrn/AACKm5QXBm2mh-2yBZDsNSnVa?dl=0
I had issue with csv, so I installed pandas and replace commends related to csv. Will this cause the issue?
Hi, I would like to simulate illumina pair-end reads for samples with different coverage following the instructions here: https://bit.ly/2XKmXcV.
However, I encountered the following error. RuleException: KeyError in line 47 of /cluster/work/pausch/group_bin/anaconda3/envs/rnftools/lib/python3.6/site-packages/rnftools/mishmash/mishmash.snake: 's not in /cluster/work/pausch/fang/low_cov/sim/ARS-UCD1.2_Btau5.0.1Y.fa.' File "/cluster/work/pausch/group_bin/anaconda3/envs/rnftools/lib/python3.6/site-packages/rnftools/mishmash/mishmash.snake", line 47, in rule_5 File "/cluster/work/pausch/group_bin/anaconda3/envs/rnftools/lib/python3.6/site-packages/rnftools/mishmash/Source.py", line 153, in create_fa File "/cluster/work/pausch/group_bin/anaconda3/envs/rnftools/lib/python3.6/site-packages/pyfaidx/init.py", line 1016, in getitem__ File "/cluster/work/pausch/group_bin/anaconda3/envs/rnftools/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job 6 since they might be corrupted: /cluster/work/pausch/fang/low_cov/sim/simulation_with_coverage_control/004/reference.fa Shutting down, this might take some time.
I am not sure how to fix this error. I'd appreciate any advice. Thanks!