Problems with a nested directory as outdir

I was running bilby_pipe and came across a problem. Let's say A is a run which has outdir=outdir and another run B which has outdir=dir1/dir2/outdir. I see that run A goes to completion, but though B finishes sampling, there are no result files that are generated in the result directory. In fact, even the checkpoint files and trace plots aren't generated. The bilby_pipe_analysis jobs go on hold after the sampling is complete.

I have reproduced this error on the Hanford cluster at /home/aditya.vijaykumar/bilby_pipe_test.

Note that the difference between the two config files is just in the outdir:

(bilby_pipe) [aditya.vijaykumar@ldas-pcdev1 bilby_pipe_test]$ diff nlive128/id1_nlive128_config_complete.ini rundir/id1/nlive128/id1_nlive128_config_complete.ini 
68c68
< outdir=/home/aditya.vijaykumar/bilby_pipe_test/nlive128
---
> outdir=/home/aditya.vijaykumar/bilby_pipe_test/rundir/id1/nlive128
(bilby_pipe) [aditya.vijaykumar@ldas-pcdev1 bilby_pipe_test]$ 

I think I have an explanation for this. In the submit/bash*sh file for run B, the bilby_pipe_analysis command reads,

/home/aditya.vijaykumar/miniconda3/envs/bilby_pipe/bin/bilby_pipe_analysis rundir/id1/nlive128/id1_nlive128_config_complete.ini --submit --outdir nlive128 --detectors H1 --detectors L1 --detectors V1 --label id1_nlive128_data0_0_analysis_H1L1V1_dynesty_par0 --data-dump-file rundir/id1/nlive128/data/id1_nlive128_data0_0_generation_data_dump.pickle --sampler dynesty

Notice the difference between the path to the *config_complete.ini and the outdir.