SilasK
commented
6 years ago Yes there are some changes between snakemake 4 and 5. for a temporary fix see #108
Closed Sofie8 closed 6 years ago
SilasK
commented
6 years ago Yes there are some changes between snakemake 4 and 5. for a temporary fix see #108
Hi , I have installed the new release 1.0.32 of atlas, I am running on 64 bit Linux, snakemake 5.1.3-py36_0 bioconda. While in the previous release it went smoothly through the samples, this throws a syntax error at the very beginning of atlas assemble, with the assemble.snakemake.
(atlas_env) : vsc31426@hpc-p-login-2 ~ 08:25 $ atlas assemble --out-dir /ddn1/vol1/site_scratch/leuven/314/vsc31426/ENG6210/atlasAA /vsc-hard-mounts/leuven-data/314/vsc31426/atlas/configAA.yaml 2>&1| tee /vsc-hard-mounts/leuven-data/314/vsc31426/scripts/atlas/20180527_atlasAA.log [2018-05-28 08:25 INFO] Executing: snakemake --snakefile /data/leuven/314/vsc31426/miniconda3/envs/atlas_env/lib/python3.6/site-packages/atlas/Snakefile --directory /ddn1/vol1/site_scratch/leuven/314/vsc31426/ENG6210/atlasAA --printshellcmds --jobs 40 --rerun-incomplete --configfile '/vsc-hard-mounts/leuven-data/314/vsc31426/atlas/configAA.yaml' --nolock --use-conda --config workflow=complete -- SyntaxError: Not all output, log and benchmark files of rule error_correction contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file. File "/data/leuven/314/vsc31426/miniconda3/envs/atlas/lib/python3.6/site-packages/atlas/Snakefile", line 177, in
File "/data/leuven/314/vsc31426/miniconda3/envs/atlas/lib/python3.6/site-packages/atlas/rules/assemble.snakefile", line 128, in
[2018-05-28 08:25 CRITICAL] Command 'snakemake --snakefile /data/leuven/314/vsc31426/miniconda3/envs/atlas_env/lib/python3.6/site-packages/atlas/Snakefile --directory /ddn1/vol1/site_scratch/leuven/314/vsc31426/ENG6210/atlasAA --printshellcmds --jobs 40 --rerun-incomplete --configfile '/vsc-hard-mounts/leuven-data/314/vsc31426/atlas/configAA.yaml' --nolock --use-conda --config workflow=complete -- ' returned non-zero exit status 1.
And the lines in the assemble.snakemake write this: (2 times {sample} in the log, while once in the benchmark), is this causing the error?:
rule error_correction: ... benchmark: "logs/benchmarks/error_correction/{sample}.txt" log: "{sample}/logs/{sample}_error_correction.log" ...
Are you experiencing the same, or how can I solve this best? Thank you, Sofie