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Hi <!subteam^S016E36N7TQ> nf-core/ampliseq just ha...
# pipeline-maintainers
d
Hi <!subteam^S016E36N7TQ> nf-core/ampliseq just had its release 2.15.0 and it would be nice if you could start the AWS test_full run to be displayed on the website. Less Important nf-core/ampliseq 2.14.0 release has also no AWS results. Additionally, nf-core/detaxizer release 1.2.0 also displays no AWS results.
j
I can see if I can do it!
First for 2.14 and then if that works 2.15
Whelp that failed:
Copy code
Command output:
  (empty)

Command error:
  7:07AM INF instance metadata ami-id=ami-08c9a28b806bde705 instance-id=i-0c1e7dd77425ef818 instance-type=c6id.32xlarge
  grep: write error: Broken pipe
  Traceback (most recent call last):
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/builtin/tools.py", line 852, in _import
      artifact = qiime2.sdk.Artifact.import_data(
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 345, in import_data
      provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 525, in __init__
      super().__init__()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 296, in __init__
      self._build_paths()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 303, in _build_paths
      self.path = qiime2.core.path.ProvenancePath()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/path.py", line 138, in __new__
      cache = get_cache()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 113, in get_cache
      _CACHE.temp_cache = Cache()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 417, in __init__
      self.__init(path=path, process_pool_lifespan=process_pool_lifespan)
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 457, in __init
      with self.lock:
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 292, in __enter__
      self.flufl_lock.lock()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/flufl/lock/_lockfile.py", line 336, in lock
      os.link(self._claimfile, self._lockfile)
  OSError: [Errno 95] Operation not supported: '/tmp/qiime2/root/LOCK|ip-172-31-11-83.eu-west-1.compute.internal|58|5400338807187908552' -> '/tmp/qiime2/root/LOCK'
  An unexpected error has occurred:
    [Errno 95] Operation not supported: '/tmp/qiime2/root/LOCK|ip-172-31-11-83.eu-west-1.compute.internal|58|5400338807187908552' -> '/tmp/qiime2/root/LOCK'
  See above for debug info.
  Fusion Info:
      fusion_version: 2.4.14-93ca7f1
      clone_namespace: false
      kernel_version: 6.1
      disk_cache_size: 7076Gb
      max_open_files: 1048576
I just specifeid 
-profile test_full,docker
, is that wrong?
(I'll try 
resulme
once_
d
Hm... QIIME2 again. Quite possible that this isnt compatible with that new AWS setup. But I cannot troubleshoot that as it is. And dont know if I should. Just to make sure try 2.15.0 and likely that fails as well, and then just omit ampliseq. If that indeed fails as well I should open an issue in ampliseq with that problem I guess.
j
OK I will try 2.15
I could try using conda instead?
d
likely it wont matter what containerization, but yes, why not.
j
Is that worth it?
d
well we should test 2.15.0 once imho, just to make sure that doesnt magically work 😉
👍 1
Thanks a lot! 2.14.0 fails in all attempts, correct? Could you try with 2.15.0 as well just to make sure?
j
2.14.0 failed wit hconda
👍 1
2.15.0 same as 2.14.0
Wait, conda error with 2.14.0 might be something else
d
But I only see 4x attempts for 2.14.0, not 2.15.0?
j
Ignore the name of the run, I used the 'profile' called 2-14-0, but switched the version
(check the configuration tab and th command)
d
ah ok 😄
j
Ah wait maybe conda isn't installed...
My only other suspicion is there is somethign to do with fusion 😬
@Rike Hanssen @Edmund
Copy code
7:15AM INF instance metadata ami-id=ami-08c9a28b806bde705 instance-id=i-03982879a77f641c4 instance-type=c6id.12xlarge
  Traceback (most recent call last):
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/builtin/tools.py", line 852, in _import
      artifact = qiime2.sdk.Artifact.import_data(
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 345, in import_data
      provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 525, in __init__
      super().__init__()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 296, in __init__
      self._build_paths()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/provenance.py", line 303, in _build_paths
      self.path = qiime2.core.path.ProvenancePath()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/path.py", line 138, in __new__
      cache = get_cache()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 113, in get_cache
      _CACHE.temp_cache = Cache()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 417, in __init__
      self.__init(path=path, process_pool_lifespan=process_pool_lifespan)
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 457, in __init
      with self.lock:
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 292, in __enter__
      self.flufl_lock.lock()
    File "/opt/conda/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/flufl/lock/_lockfile.py", line 336, in lock
      os.link(self._claimfile, self._lockfile)
  OSError: [Errno 95] Operation not supported: '/tmp/qiime2/root/LOCK|ip-172-31-40-202.eu-west-1.compute.internal|66|1690664243289351086' -> '/tmp/qiime2/root/LOCK'
  An unexpected error has occurred:
    [Errno 95] Operation not supported: '/tmp/qiime2/root/LOCK|ip-172-31-40-202.eu-west-1.compute.internal|66|1690664243289351086' -> '/tmp/qiime2/root/LOCK'
  See above for debug info.
Writing a lock file issue?
I'll try a non-fusion run
It's fusionb 😆
screams 1
QIIME is happyn ow (2.14)
d
uff, aweome!
j
OK 2.14 ran through
🎉 1
Now trying 2.15
d
succeeded, thanks a lot!
p
@James Fellows Yates any chance you could put the error + log files onto the Nextflow slack 
#fusion-fs
channel please, with the pipeline / version etc to reproduce?
We don't have a great way to collect these Fusion errors currently but I would like to
I guess that the one you hit has already been fixed, as it sounds like one I recognise, but it'd be good to confirm.
j
Which channel? 🤔
p
Nextflow slack, 
#fusion-fs
j
ah
e
For anyone else finding this in the future
Open in Slack
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