Color matrix < ~Data/Intensities/BaseCalls/Matrix/s_1_3_1117_matrix.txt > could not be open

[tvincent07]

Hi,
i'm sorry to write another post but I resolved my last error post by adding

ENV PYTHONPATH /opt/tailseeker:$PYTHONPATH
to the Dockerfile and by creating a new docker image.
The thing is I quickly have another mistake more difficult to solve (for me) :

Color matrix </home/tvincent/Helene/run1Miseq4/runMiseq1/160808_M03768_0018_000000000-AMUBW/Data/Intensities/BaseCalls/Matrix/s_1_3_1117_matrix.txt> could not be opened.
Error in job process_signals while creating output files scratch/sigproc-conf/a1117.ini, scratch/taginfo/e00_a1117.txt.gz, scratch/taginfo/e05_a1117.txt.gz, scratch/taginfo/e10_a1117.txt.gz, scratch/taginfo/e100_a1117.txt.gz, scratch/taginfo/e105_a1117.txt.gz, scratch/taginfo/e110_a1117.txt.gz, 

etc, the list is long.

scratch/signals/spk64_a1117.sigpack, scratch/signals/spk8_a1117.sigpack, scratch/signals/spkN_a1117.sigpack, scratch/stats/signal-proc-a1117.csv.
RuleException:
CalledProcessError in line 200 of /opt/tailseeker/tailseeker/main.py:
Command '/opt/tailseeker/bin/tailseq-import scratch/sigproc-conf/a1117.ini' returned non-zero exit status 255
  File "/opt/tailseeker/tailseeker/main.py", line 200, in __rule_process_signals
  File "/usr/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Exiting because a job execution failed. Look above for error message
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

I checked and the matrix file location is the good one. I don't understand why it cannot be open.
Thanks for replying me.
best
Timothée

[hyeshik]

The location of data must be accessible from the Docker container. With the default wrapper script, the data files are exposed as /data.

[tvincent07]

I was confused between the two data location path you have to fill.
In the environment variable TAILSEEKER_DATADIR, you have to give the path to your Hiseq/Miseq output directory
export TAILSEEKER_DATADIR=/home/user/runMiseq/161206_G02868_0017_000000000-AMCBY
But in the tailseeker.yaml file, the dir subsection must be fill with "/data" and nothing else.