Hoohm
commented
6 years ago Hello. Thanks for the report. I actually updated the env for ggplot2 a couple of hours ago. Try it with the new one. I think it came with the ggplo2 3.0 update. Now ggplot2 is fixed and I've added the missing fortranlib.
To be in the safe side, I would delete the plot env so that it downloads it from scratch.
If you still have issues after the update, could you please add the logfiles that show the R error and not the snakemake log.
Thank you
On Tue, Jul 17, 2018, 19:59 terooatt notifications@github.com wrote:
Hi,
Dropseqpipe worked well for me couple months ago but recently after I have updated it it keeps on stoping when it starts using the Rscripts. It looks like some conda environments are incompatible with some R libraries such ggplot2, I think. Anyways here is the error I get, can you help. Thank you very much.
localrule plot_BC_drop: input: logs/Human_mouse_0.25M_CELL_barcode.txt, logs/Human_mouse_0.25M_UMI_barcode.txt, logs/Human_mouse_0.25M_reads_left.txt, logs/Human_mouse_0.25M_reads_left_trim.txt output: plots/BC_drop.pdf jobid: 22
Activating conda environment: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 Activating conda environment: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 Error in rule plot_yield: jobid: 31 Error in rule plot_BC_drop: output: plots/yield.pdf jobid: 22 conda-env: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 output: plots/BC_drop.pdf
conda-env: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70RuleException: CalledProcessError in line 165 of /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/map.smk: Command 'source activate /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70; set -euo pipefail; Rscript /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/scripts/.snakemake.fx15wxlz.plot_yield.R ' returned non-zero exit status 1. File "/home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/map.smk", line 165, in rule_plot_yield File "/home/tommy/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 55, in run RuleException: CalledProcessError in line 258 of /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/filter.smk: Command 'source activate /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70; set -euo pipefail; Rscript /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/scripts/.snakemake.7qdvqpqr.plot_BC_drop.R ' returned non-zero exit status 1. File "/home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/filter.smk", line 258, in rule_plot_BC_drop File "/home/tommy/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 55, in run Removing temporary output file data/Human_mouse_0.25M/Aligned.out.bam. Finished job 57.
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terooatt
Hi,
Dropseqpipe worked well for me couple months ago but recently after I have updated it it keeps on stoping when it starts using the Rscripts. It looks like some conda environments are incompatible with some R libraries such ggplot2, I think. Anyways here is the error I get, can you help. Thank you very much.
localrule plot_BC_drop: input: logs/Human_mouse_0.25M_CELL_barcode.txt, logs/Human_mouse_0.25M_UMI_barcode.txt, logs/Human_mouse_0.25M_reads_left.txt, logs/Human_mouse_0.25M_reads_left_trim.txt output: plots/BC_drop.pdf jobid: 22
Activating conda environment: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 Activating conda environment: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 Error in rule plot_yield: jobid: 31 Error in rule plot_BC_drop: output: plots/yield.pdf jobid: 22 conda-env: /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70 output: plots/BC_drop.pdf
RuleException: CalledProcessError in line 165 of /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/map.smk: Command 'source activate /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70; set -euo pipefail; Rscript /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/scripts/.snakemake.fx15wxlz.plot_yield.R ' returned non-zero exit status 1. File "/home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/map.smk", line 165, in rule_plot_yield File "/home/tommy/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 55, in run RuleException: CalledProcessError in line 258 of /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/filter.smk: Command 'source activate /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/.snakemake/conda/122c4b70; set -euo pipefail; Rscript /home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/scripts/.snakemake.7qdvqpqr.plot_BC_drop.R ' returned non-zero exit status 1. File "/home/tommy/Nadia5_mix_human_mouse/dropSeqPipe/rules/filter.smk", line 258, in rule_plot_BC_drop File "/home/tommy/miniconda3/envs/dropSeqPipe/lib/python3.6/concurrent/futures/thread.py", line 55, in run Removing temporary output file data/Human_mouse_0.25M/Aligned.out.bam. Finished job 57.