search

faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
Other
78 stars 49 forks source link

Assembly (velvet/abyss) not being able to detect fastq.gz? #125

Closed ghost closed 6 years ago

ghost commented 6 years ago

I am running the tutorial on our cluster, and at the assembly step I am getting the following error:

Traceback (most recent call last): File "/apps/phyluce/20180727/bin/phyluce_assembly_assemblo_velvet", line 259, in main() File "/apps/phyluce/20180727/bin/phyluce_assembly_assemblo_velvet", line 240, in main reads = get_input_files(dir, args.subfolder, log) File "/apps/phyluce/20180727/lib/python2.7/site-packages/phyluce/raw_reads.py", line 92, in get_input_files raise IOError("There are not appropriate files in {}".format(dir)) IOError: There are not appropriate files in /ufrc/lucky/yuanmeng.zhang/uce-tutorial/clean-fastq/alligator_mississippiensis/split-adapter-quality-trimmed

Even though I have singleton.fastq.gz, READ1.fastq.gz, and READ2.fastq.gz in the split-adapter-quality-trimmed folder. I tried using both velvet and abyss and I get the same results.

ghost commented 6 years ago

Ah okay so not creating subfolder was the key. Seems to be working now.