TypeError: sequence item 4: expected string, NoneType found

[jwidmann]

Hi, I tried running dammit after updating via sudo pip install -U dammit with the command dammit annotate TrinityNormalizedTissues.fasta --n_threads 2 --busco-group eukaryota and get the following Error message: Traceback (most recent call last): File "/usr/local/bin/dammit", line 10, in <module> app.DammitApp(arg_src=sys.argv[1:]).run() File "/usr/local/lib/python2.7/dist-packages/dammit/app.py", line 31, in run self.args.func() File "/usr/local/lib/python2.7/dist-packages/dammit/app.py", line 212, in handle_annotate annotate.AnnotateHandler(self.args, db_handler.databases).handle() File "/usr/local/lib/python2.7/dist-packages/dammit/annotate.py", line 49, in __init__ self.tasks = list(self.get_tasks()) File "/usr/local/lib/python2.7/dist-packages/dammit/annotate.py", line 261, in get_tasks for task in self.transdecoder_tasks(): File "/usr/local/lib/python2.7/dist-packages/dammit/annotate.py", line 181, in transdecoder_tasks n_nodes=self.args.n_nodes) File "/usr/local/lib/python2.7/dist-packages/dammit/tasks.py", line 88, in d_to_t ret_dict = task_dict_func(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/dammit/tasks.py", line 473, in get_hmmscan_task parallel_cmd = parallel_fasta(input_filename, n_threads) File "/usr/local/lib/python2.7/dist-packages/dammit/tasks.py", line 56, in parallel_fasta return ' '.join(cmd) TypeError: sequence item 4: expected string, NoneType found The temporary files are called TRINITY_DNxxxxx_cx_gxixNone.temp How can I solve this? Greetings

[jwidmann]

I'm really sorry, I just forgot to install parallel.. Sorry for stealing your time.

[camillescott]

Hi @jwidmann! I'm actually going to reopen this so I can add a check for parallel to the dependency handler. Thanks for filing!

[camillescott]

Fixed in 1.0 beta; closing.