Comments (9)
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?
from pgap.
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!
from pgap.
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
from pgap.
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.
from pgap.
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!
from pgap.
Hi
Yes, it is a Mac system.
I'll take a look at #276 and wait for the response of your team,
Thanks!
from pgap.
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
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Thank you for adding new data, user @juansebe1 ! This is very helpful!
from pgap.
Unfortunately, we have not been able to reproduce this error on our end
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Related Issues (20)
- [BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments HOT 8
- [BUG] -c flag not received: /mnt/shared/scratch/theaven/uncompressed/hogenhout/pgap-s7 HOT 1
- product protein name issues HOT 3
- [BUG] Final process status is permanentFail HOT 1
- [Error] Docker exited with rc = 1 HOT 3
- [Error] Docker exited with rc =1 HOT 2
- Get_Proteins_app issues HOT 14
- Error: Final process status is permanentFail HOT 7
- Error: Final process status is permanentFail HOT 17
- source code for gc_get_molecules HOT 2
- PGAP for multiple users HOT 2
- ORF prediction issue HOT 3
- [BUG] Genus species requirement HOT 8
- [BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default HOT 4
- Species_Requirement_option HOT 1
- [BUG] Failing to run some sequences HOT 2
- [BUG] FATAL: "cwltool": executable file not found in $PATH in 2024-04-27.build7426 HOT 4
- [BUG] GFF3 output file does not contain sequence-region name HOT 3
- [BUG] PGAP failed, docker exited with rc = 1 HOT 11
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