Hoohm
commented
7 years ago Hello,
you probably have a mispelling in the config.yaml from the run.
Can you double check the spelling?
allowed_aligner_mismatch
Closed abmmki closed 6 years ago
Hoohm
commented
7 years ago Hello,
you probably have a mispelling in the config.yaml from the run.
Can you double check the spelling?
allowed_aligner_mismatch
Hi
can you help to solve the following problem. I am using latest version 0.23a
dropSeqPipe -f /hd2/ -c /home/dropSeqPipe/local.yaml -m pre-process
[Tue Sep 19 09:00:33 CDT 2017] picard.sam.SamToFastq done. Elapsed time: 16.92 minutes. Runtime.totalMemory()=1126170624 [Tue Sep 19 09:00:33 2017] Finished job 1. [Tue Sep 19 09:00:33 2017] 3 of 4 steps (75%) done [Tue Sep 19 09:00:33 2017] [Tue Sep 19 09:00:33 2017] localrule all: input: wts3_tagged_unmapped.fastq.gz jobid: 0 [Tue Sep 19 09:00:33 2017] [Tue Sep 19 09:00:33 2017] Finished job 0. [Tue Sep 19 09:00:33 2017] 4 of 4 steps (100%) done Running Alignement [Tue Sep 19 09:00:33 2017] KeyError in line 23 of /usr/lib/python3.4/site-packages/dropSeqPipe/Snakefiles/singleCell/star_align.snake: 'allowed_aligner_mismatch' File "/usr/lib/python3.4/site-packages/dropSeqPipe/Snakefiles/singleCell/star_align.snake", line 23, in
Plotting STAR logs
Error in file(file, "rt") : cannot open the connection
Calls: star.logs -> read.table -> file
In addition: Warning message:
In file(file, "rt") : cannot open file 'NA': No such file or directory
Execution halted
Traceback (most recent call last):
File "/bin/dropSeqPipe", line 9, in
load_entry_point('dropSeqPipe==0.23a0', 'console_scripts', 'dropSeqPipe')()
File "/usr/lib/python3.4/site-packages/dropSeqPipe/main.py", line 150, in main
shell(star_summary)
File "/usr/lib/python3.4/site-packages/snakemake-3.10.1-py3.4.egg/snakemake/shell.py", line 80, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'Rscript /usr/lib/python3.4/site-packages/dropSeqPipe/Rscripts/STAR_log_plot.R /hd2/' returned non-zero exit status 1