Fast5_to_seq_summary error
apeltzer opened this issue · comments
Describe the bug
Running like this:
Fast5_to_seq_summary -f FAST5 -t 8 -s './sequencing_summary.txt' --verbose_level 2
pycoQC -f "sequencing_summary.txt" -o pycoQC_BGLUMAE.html -j pycoQC_BGLUMAE.json
Results in:
[WORKER_02] Start processing fast5 files
[WORKER_03] Start processing fast5 files
[WORKER_04] Start processing fast5 files
[WORKER_05] Start processing fast5 files
An error occured. All processes were killed
Traceback (most recent call last):
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/bin/Fast5_to_seq_summary", line 12, in <module>
sys.exit(main_Fast5_to_seq_summary())
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/lib/python3.7/site-packages/pycoQC/__main__.py", line 165, in main_Fast5_to_seq_summary
verbose_level = args.verbose_level)
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/lib/python3.7/site-packages/pycoQC/Fast5_to_seq_summary.py", line 162, in __init__
raise E
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/lib/python3.7/site-packages/pycoQC/Fast5_to_seq_summary.py", line 152, in __init__
raise pycoQCError(tb)
pycoQC.common.pycoQCError: Traceback (most recent call last):
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/lib/python3.7/site-packages/pycoQC/Fast5_to_seq_summary.py", line 206, in _read_fast5
"raw_read" : "/Raw/Reads/{}/".format(list(h5_fp["/Raw/Reads"].keys())[0]),
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/opt/conda/envs/nf-core-bacass-1.1.0dev/lib/python3.7/site-packages/h5py/_hl/group.py", line 262, in __getitem__
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: 'Unable to open object (component not found)'- OS: (e.g. iOS) CentOS7
Latest pycoQC 2.5 from Conda
I have the same issue under Ubuntu 16.04.6 LTS
pycoQC 2.5.0.17 installed using conda
Hi both.
Are you using multi-fast5 as input for Fast5_to_seq_summary ?
Missing the experience to comment on this properly, so I'm asking here: I have many FAST5 files in a folder, does that mean this is multi-fast5 input automatically? The help text talking about multi-fast5 reads a bit differently, which is why I'm not sure "many reads per fast5 file..."
Maybe I am - can check when I know what that actually means 😆
Sry, No Fast5 format is a recent version (1year old) of ONT raw file format. Essentially it means that each file contains multiple reads in it as opposed to the previous version where 1 file = 1 read.
You can check by opening a file with for example https://www.hdfgroup.org/downloads/hdfview/
I haven't implemented multifast5 support in Fast5_to_seq_summary and I don't have any plans to do it any soon. You can generate a new seq summary file by re-basecalling your data with Guppy.
Can you confirm this is a multi fast5 issue ?
Sorry, will check tomorrow at work - I guess thats probably the reason 😓 Demultiplexing was done with a newer Guppy version at least ...
Looks like it - thanks!
Hi. I am having the same issue while providing a list of FAST5 files like the one below, although in my case it does not start the analysis. It jumps straight to the error.
The version is the latest v2.5.2 installed with Conda, which now includes the option.
~/input/fast5$ ls
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_0.fast5
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_59.fast5
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_1.fast5
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_6.fast5
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_10.fast5
GXB01322_20181213_FAK35814_GA20000_sequencing_run_Run00012_MIN106_RBK004_17047_60.fast5
...