[BUG] Fail in GenBank output file

[juansebe1]

Why does pgap does not give me the GenBank (.gb) file in the output?

[azat-badretdin]

Thank you for your report, user @juansebe1 !

Do you have a file with .gbk extension? If not, could you please provide details of your run, if the file cwltool.log contains permanentFail and 100 lines of log preceding the first permanentFail in this log file?

[juansebe1]

No, I don't have a .gbk file Can I share you the cwltool.log file and see what you are asking ? Yes, it contains permanentFail Thanks!

cwltool.log.zip

[azat-badretdin]

For the record, this is the relevant part:

+ /root/venv/bin/checkm taxonomy_wf -t 1 -g -x fa domain Bacteria bins-prot/ taxonomy_wf-prot/
Process SyncManager-1:
Traceback (most recent call last):
  File "/opt/python-3.9/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/opt/python-3.9/lib/python3.9/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/python-3.9/lib/python3.9/multiprocessing/managers.py", line 583, in _run_server
    server = cls._Server(registry, address, authkey, serializer)
  File "/opt/python-3.9/lib/python3.9/multiprocessing/managers.py", line 156, in __init__
    self.listener = Listener(address=address, backlog=16)
  File "/opt/python-3.9/lib/python3.9/multiprocessing/connection.py", line 448, in __init__
    self._listener = SocketListener(address, family, backlog)
  File "/opt/python-3.9/lib/python3.9/multiprocessing/connection.py", line 591, in __init__
    self._socket.bind(address)
PermissionError: [Errno 1] Operation not permitted
Traceback (most recent call last):
  File "/root/venv/bin/checkm", line 856, in <module>
    checkmParser.parseOptions(args)
  File "/root/venv/lib/python3.9/site-packages/checkm/main.py", line 992, in parseOptions
    self.analyze(options)
  File "/root/venv/lib/python3.9/site-packages/checkm/main.py", line 326, in analyze
    binIdToModels = mgf.find(binFiles,
  File "/root/venv/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 68, in find
    binIdToModels = mp.Manager().dict()
  File "/opt/python-3.9/lib/python3.9/multiprocessing/context.py", line 57, in Manager
    m.start()
  File "/opt/python-3.9/lib/python3.9/multiprocessing/managers.py", line 558, in start
    self._address = reader.recv()
  File "/opt/python-3.9/lib/python3.9/multiprocessing/connection.py", line 250, in recv
    buf = self._recv_bytes()
  File "/opt/python-3.9/lib/python3.9/multiprocessing/connection.py", line 414, in _recv_bytes
    buf = self._recv(4)
  File "/opt/python-3.9/lib/python3.9/multiprocessing/connection.py", line 383, in _recv
    raise EOFError
EOFError

[azat-badretdin]

This looks similar to the issue #276 and judging by the user host mounted dirs, this is also a Mac system.

Issue #276 was closed as de facto unresolved, the user did not reply for two months.

[azat-badretdin]

As you can see I labeled this Issue with our internal ticket created based on #276

Someone from our team will have a look.

Thank you for your patience!

[juansebe1]

Hi Yes, it is a Mac system. I'll take a look at https://github.com/ncbi/pgap/issues/276 and wait for the response of your team, Thanks!

[juansebe1]

Hi! I've tried again with the same genome and with another from the GenBank, and I could not obtain a .gbk file neither. I'll share with you the cwltool.log file and the genome in .fasta extension, so if you can see what I'm doing wrong,

thank you cwltool.log.zip fle_am.fasta.zip

[azat-badretdin]

Thank you for adding new data, user @juansebe1 ! This is very helpful!

[azat-badretdin]

Unfortunately, we have not been able to reproduce this error on our end