running FAMLI with singularity and permission denied to /root/ncbi

[ralsallaq]

Hi, I am trying to run FAMLI using singularity. Using the test example singularity run -B tests:/share famli_latest.sif famli
align
--input /share/example.fastq
--sample-name example
--ref-db /share/refdb.dmnd
--output-folder /share/
--blocks 5
--query-gencode 11
--threads 16
--min-qual 30
--temp-folder /share/ I got the following output: 2019-11-22 15:42:36,764 INFO [FAMLI] Checking for a working copy of DIAMOND 2019-11-22 15:42:36,764 INFO [FAMLI] Commands: 2019-11-22 15:42:36,764 INFO [FAMLI] diamond --version 2019-11-22 15:42:36,790 INFO [FAMLI] Standard output of subprocess: 2019-11-22 15:42:36,791 INFO [FAMLI] diamond version 0.9.10 2019-11-22 15:42:36,791 INFO [FAMLI] 2019-11-22 15:42:36,791 INFO [FAMLI] Getting reference database from local path: /share/refdb.dmnd 2019-11-22 15:42:36,791 INFO [FAMLI] Setting up fastq-dump cache within /share/11ec9d1a Traceback (most recent call last): File "/usr/local/bin/famli", line 9, in load_entry_point('famli==1.0', 'console_scripts', 'famli')() File "/usr/local/lib/python2.7/dist-packages/famli/run_famli.py", line 387, in main FAMLI() File "/usr/local/lib/python2.7/dist-packages/famli/run_famli.py", line 43, in init self.align() File "/usr/local/lib/python2.7/dist-packages/famli/run_famli.py", line 150, in align set_up_sra_cache_folder(temp_folder) File "/usr/local/lib/python2.7/dist-packages/famli/fastq_helpers.py", line 50, in set_up_sra_cache_folder os.mkdir(path) OSError: [Errno 13] Permission denied: '/root/ncbi' So it is trying to create /root/ncbi directory which of course is denied. Any idea why is this happening? Thanks so much for this great promising repository