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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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tsv stats error #260

Closed bernt-matthias closed 3 years ago

bernt-matthias commented 3 years ago

For the following call NanoPlot --tsv_stats --fasta read_0.fasta read_1.fasta -o '.' I get:

Traceback (most recent call last):
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/bin/NanoPlot", line 10, in <module>
    sys.exit(main())
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanoplot/NanoPlot.py", line 77, in main
    settings["statsfile"] = [make_stats(datadf, settings, suffix="", tsv_stats=args.tsv_stats)]
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanoplot/NanoPlot.py", line 119, in make_stats
    stats_df = nanomath.write_stats(
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanomath/nanomath.py", line 181, in write_stats
    df = pd.DataFrame([s.to_dict() for s in stats]).transpose()
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanomath/nanomath.py", line 181, in <listcomp>
    df = pd.DataFrame([s.to_dict() for s in stats]).transpose()
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanomath/nanomath.py", line 91, in to_dict
    self.unwind_long_features_top5(feature='_top5_lengths', name='longest_read_(with_Q)')
  File "/home/berntm/miniconda3/envs/__nanoplot@1.36.2/lib/python3.9/site-packages/nanomath/nanomath.py", line 98, in unwind_long_features_top5
    for entry, label in zip(self.__dict__[feature], range(1, 6)):
KeyError: '_top5_lengths'

The call does not crash without --tsv_stats

wdecoster commented 3 years ago

Thanks for reporting and my apologies for the inconvenience. It seems that the issue is only triggered when fasta is used as input, hence it escaped detection for a long time. It has now been fixed in nanomath v1.2.1 (pushed to PyPI, probably soon updated on bioconda).

Cheers, Wouter

bernt-matthias commented 3 years ago

Thanks. Just bumped the recipe https://github.com/bioconda/bioconda-recipes/pull/28433

bernt-matthias commented 3 years ago

May I just ask another question here. I'm working on the Galaxy tool wrapper for NanoPlot. I have the problem that the png images are not generated in the containerized tests. I guess there is some library missing in the requirements of the NanoPlot recipe. Any idea what this could be?

wdecoster commented 3 years ago

Can you access the log file? Does the process have Internet access while running? Kaleido is used for the png images, and similar problems have been reported...

bernt-matthias commented 3 years ago

The log file says: 

2021-05-11 15:16:57,812 No static plots are saved due to some kaleido problem:
2021-05-11 15:16:57,812 Failed to start Kaleido subprocess. Error stream:

[0511/151657.584631:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale 
[0511/151657.602031:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale 
[0511/151657.603772:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale 
[0511/151657.604856:WARNING:discardable_shared_memory_manager.cc(194)] Less than 64MB of free space in temporary directory for shared memory files: 0
[0511/151657.625941:ERROR:platform_shared_memory_region_posix.cc(250)] Creating shared memory in .org.chromium.Chromium.DGgLi9 failed: Permission denied (13)
[0511/151657.626020:ERROR:platform_shared_memory_region_posix.cc(253)] Unable to access(W_OK|X_OK) .: Permission denied (13)
Received signal 6
#0 0x55c8fbc3ed79 base::debug::CollectStackTrace()
#1 0x55c8fbbbc633 base::debug::StackTrace::StackTrace()
#2 0x55c8fbc3e95b base::debug::(anonymous namespace)::StackDumpSignalHandler()
#3 0x7f4379a9c730 (/lib/x86_64-linux-gnu/libpthread-2.28.so+0x1272f)
#4 0x7f437958a7bb gsignal
#5 0x7f4379575535 abort
#6 0x55c8fbbea30a base::internal::OnNoMemoryInternal()
#7 0x55c8fbbea329 base::(anonymous namespace)::OnNoMemory()
#8 0x55c8fbbea319 base::TerminateBecauseOutOfMemory()
#9 0x55c8fbbd40ab base::FieldTrialList::InstantiateFieldTrialAllocatorIfNeeded()
#10 0x55c8fbbd4239 base::FieldTrialList::CopyFieldTrialStateToFlags()
#11 0x55c8fa72ff82 content::GpuProcessHost::LaunchGpuProcess()
#12 0x55c8fa72e910 content::GpuProcessHost::Init()
#13 0x55c8fa72e6c2 content::GpuProcessHost::Get()
#14 0x55c8fab4bb6e base::internal::Invoker<>::RunOnce()
#15 0x55c8fbc02306 base::TaskAnnotator::RunTask()
#16 0x55c8fbc13cf6 base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::DoWorkImpl()
#17 0x55c8fbc139ea base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::DoWork()
#18 0x55c8fbc60899 base::MessagePumpLibevent::Run()
#19 0x55c8fbc1459b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run()
#20 0x55c8fbbed9bd base::RunLoop::Run()
#21 0x55c8fa5d5f18 content::BrowserProcessSubThread::IOThreadRun()
#22 0x55c8fbc2c874 base::Thread::ThreadMain()
#23 0x55c8fbc4ecaa base::(anonymous namespace)::ThreadFunc()
#24 0x7f4379a91fa3 start_thread
#25 0x7f437964c4cf clone
  r8: 0000000000000000  r9: 00007f437738cf50 r10: 0000000000000008 r11: 0000000000000246
 r12: 000055c8f8620780 r13: 000055c8f8562eb0 r14: 00001839a42f6cc0 r15: 00001839a4327240
  di: 0000000000000002  si: 00007f437738cf50  bp: 00007f437738d1b0  bx: 0000000000000006
  dx: 0000000000000000  ax: 0000000000000000  cx: 00007f437958a7bb  sp: 00007f437738cf50
  ip: 00007f437958a7bb efl: 0000000000000246 cgf: 002b000000000033 erf: 0000000000000000
 trp: 0000000000000000 msk: 0000000000000000 cr2: 0000000000000000
[end of stack trace]
Calling _exit(1). Core file will not be generated.
wdecoster commented 3 years ago

So indeed a kaleido problem, unfortunately. These errors are intercepted to make sure they don't crash NanoPlot itself.

bernt-matthias commented 3 years ago

Could solve it by exporting the TMPDIR variable.

wdecoster commented 3 years ago

Glad to hear that! Thanks for the feedback.