I am running into a problem with singularity where some file (MetricsOutput.tsv) cannot be found within the container. Maybe this is related to the -B command? The path provided with the -m command is correct. Any ideas about the reason for the error?
singularity exec \
--no-home \
-B /mnt/archive/username/software/TSO:/proj/data \
-W /mnt/archive/username/software/TSO \
my_singularity.sif \
bash /proj/scripts/process.sh \
-m /mnt/archive/username/software/TSO/sample_data/analysis_results/Results/MetricsOutput.tsv \
-r /mnt/archive/username/software/TSO/sample_data/sequences/data/RunCompletionStatus.xml \
-l data \
-o /mnt/archive/username/software/TSO/sample_data/analysis_results/metrics_plots \
--create_plots False \
--host_system_mounting_directory /mnt/archive/username/software/TSO
Error:
[PROJ Python lib module - ERROR] Specified metrics file("/proj/data//sample_data/analysis_results/Results/MetricsOutput.tsv") couldn't be located within the container. Exiting.