copy_and_build_index error in phyluce mapping

[kmontana13]

Hello! I am getting the following error when I run this command in my directory that contains directories for my raw reads and UCE contigs: phyluce_workflow --config mapping_config_Sept13_24_spaces.yaml --output rc_output --workflow mapping --cores 10

Building DAG of jobs...
MissingInputException in line 39 of /home/kmontana/miniconda3/envs/phyluce-1.7.1/phyluce/workflows/mapping/Snakefile:
Missing input files for rule copy_and_build_index: contigs/a_2233_3.unaligned.fasta

The raw reads are formatted like this, for example: with in the a_2233_3 directory you will find, A_2233_3_CKDL220032227-1A_HTH5LDSX5_L3_1.fq.gz and A_2233_3_CKDL220032227-1A_HTH5LDSX5_L3_2.fq.gz . The contigs are formatted like this, for example: a_2233_3.unaligned.fasta .

I have followed the config file format, used relative paths for my files and am 100% sure the paths are right, the file is not a symlink, and I removed - and replaced with _ . I also tried running the command on just one sample and got the same error. You can find my .yaml config file copied below; just changed .yaml to .txt so I could upload here.

Thank you for any insight you can provide to help with this issue!

mapping_config_Sept13_24_spaces.txt