Issue with tabulate

[notlob91]

Hi, I'm trying to use Ananke on some time series data I have, but I've run across some issues during the "tabulate" step. Any help would be much appreciated!

My command:
ananke tabulate -i /mnt/maximus/data1/biddle/JGI_mat_amplicon/Raw_Data/FB/rep_set_q29.fna -o FB_ananke_db.h5 -f FB_seq.unique.fasta -m /home/kbousses/ananke-master/mapping_FB.txt -t time_points

The error:

Traceback (most recent call last): File "/home/kbousses/miniconda/bin/ananke", line 11, in <module> load_entry_point('ananke==0.3.0', 'console_scripts', 'ananke')() File "/home/kbousses/miniconda/lib/python3.4/site-packages/ananke-0.3.0-py3.4.egg/ananke/ananke.py", line 159, in main fasta_to_ananke(args.i, args.m, args.t, args.o, args.f, args.multi, args.size_labels) File "/home/kbousses/miniconda/lib/python3.4/site-packages/ananke-0.3.0-py3.4.egg/ananke/_tabulate.py", line 238, in fasta_to_ananke timeseriesdb = TimeSeriesData(timeseriesdata_path) File "/home/kbousses/miniconda/lib/python3.4/site-packages/ananke-0.3.0-py3.4.egg/ananke/_database.py", line 66, in __init__ maxshape=(None,None), exact=False, fillvalue=-2) File "/home/kbousses/miniconda/lib/python3.4/site-packages/h5py/_hl/group.py", line 126, in require_dataset return self.create_dataset(name, *(shape, dtype), **kwds) File "/home/kbousses/miniconda/lib/python3.4/site-packages/h5py/_hl/group.py", line 105, in create_dataset dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) File "/home/kbousses/miniconda/lib/python3.4/site-packages/h5py/_hl/dataset.py", line 129, in make_new_dset dset_id = h5d.create(parent.id, None, tid, sid, dcpl=dcpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696) File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654) File "h5py/h5d.pyx", line 79, in h5py.h5d.create (/home/ilan/minonda/conda-bld/work/h5py/h5d.c:1969) ValueError: Unable to create dataset (No appropriate function for conversion path)

[loulanomics]

Hi, I am having this same issue. Was this ever resolved? Thank you!

[ctekellogg]

I'm also having a similar issue when using ananke import_from_dada2 . Not sure if I have my file structure wrong (since i didn't import directly from dada2 but rather from a phyloseq ASV table generated from dada2 merged and denoised reads in qiime2).

My data structure for the ASV table is: samples as rows and asv as columns (where the asv name is the sequence). The data structure for the metadata is samples as rows and info, including time_points as columns. My understanding is that the -f and -o files are output by import_from_dada2 with the name I give them (at first i thought i had to provide at -f file but now i gather it is generated by this function.

$ ananke import_from_dada2 -i qu39_otus_an
anke.csv -m qu39_metadata_time.txt -t time_points -f seq.unique.dada2.fasta -o 
qu39_ananke.h5
Creating required data sets in new HDF5 file at qu39_ananke.h5
Traceback (most recent call last):
  File "/Users/colleen.kellogg/miniconda2/bin/ananke", line 11, in <module>
    load_entry_point('ananke==0.3.0', 'console_scripts', 'ananke')()
  File "/Users/colleen.kellogg/.local/lib/python2.7/site-packages/ananke-0.3.0-py2.7.egg/ananke/ananke.py", line 161, in main
    dada2_to_ananke(args.i, args.m, args.t, args.o, args.f, args.multi)
  File "/Users/colleen.kellogg/.local/lib/python2.7/site-packages/ananke-0.3.0-py2.7.egg/ananke/_tabulate.py", line 321, in dada2_to_ananke
    timeseriesdb = TimeSeriesData(timeseriesdata_path)
  File "/Users/colleen.kellogg/.local/lib/python2.7/site-packages/ananke-0.3.0-py2.7.egg/ananke/_database.py", line 66, in __init__
    maxshape=(None,None), exact=False, fillvalue=-2)
  File "/Users/colleen.kellogg/miniconda2/lib/python2.7/site-packages/h5py/_hl/group.py", line 191, in require_dataset
    return self.create_dataset(name, *(shape, dtype), **kwds)
  File "/Users/colleen.kellogg/miniconda2/lib/python2.7/site-packages/h5py/_hl/group.py", line 136, in create_dataset
    dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
  File "/Users/colleen.kellogg/miniconda2/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 167, in make_new_dset
    dset_id = h5d.create(parent.id, None, tid, sid, dcpl=dcpl)
  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/h5d.pyx", line 80, in h5py.h5d.create
ValueError: Unable to create dataset (no appropriate function for conversion path)

Any help would be so appreciated!

Thank you,
colleen

[Fmiranda86]

Same here, have you solved it?

Creating required data sets in new HDF5 file at ananke_db_0.h5 Traceback (most recent call last): File "/home/fmiranda/.local/bin/ananke", line 11, in <module> load_entry_point('ananke==0.3.0', 'console_scripts', 'ananke')() File "/home/fmiranda/.local/lib/python3.6/site-packages/ananke-0.3.0-py3.6.egg/ananke/ananke.py", line 161, in main dada2_to_ananke(args.i, args.m, args.t, args.o, args.f, args.multi) File "/home/fmiranda/.local/lib/python3.6/site-packages/ananke-0.3.0-py3.6.egg/ananke/_tabulate.py", line 321, in dada2_to_ananke timeseriesdb = TimeSeriesData(timeseriesdata_path) File "/home/fmiranda/.local/lib/python3.6/site-packages/ananke-0.3.0-py3.6.egg/ananke/_database.py", line 66, in __init__ maxshape=(None,None), exact=False, fillvalue=-2) File "/home/fmiranda/miniconda3/envs/picrust2/lib/python3.6/site-packages/h5py/_hl/group.py", line 191, in require_dataset return self.create_dataset(name, *(shape, dtype), **kwds) File "/home/fmiranda/miniconda3/envs/picrust2/lib/python3.6/site-packages/h5py/_hl/group.py", line 136, in create_dataset dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) File "/home/fmiranda/miniconda3/envs/picrust2/lib/python3.6/site-packages/h5py/_hl/dataset.py", line 167, in make_new_dset dset_id = h5d.create(parent.id, None, tid, sid, dcpl=dcpl) 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/h5d.pyx", line 80, in h5py.h5d.create ValueError: Unable to create dataset (no appropriate function for conversion path)

Thanks,
Fabi

[raphenya]

Software dependecies used:

Package         Version
--------------- -------
ananke          0.3.0  
bitarray        1.2.0  
colorlover      0.3.0  
Cython          0.29.14
h5py            2.10.0 
joblib          0.14.1 
numpy           1.18.0 
paho-mqtt       1.5.0  
pandas          0.25.3 
pip             9.0.1  
pkg-resources   0.0.0  
plotly          4.4.1  
python-dateutil 2.8.1  
pytz            2019.3 
retrying        1.3.3  
scikit-learn    0.22.1 
scipy           1.4.1  
setuptools      39.0.1 
six             1.13.0 
wheel           0.30.0 

Generated tab / csv file from https://github.com/beiko-lab/ananke/wiki/Importing-Denoised-Sequences-from-DADA2 but only using 16 fastqs

METADATA_time.txt

dada2_export.csv.zip

Import command:

ananke import_from_dada2 \
-i dada2_export.csv \
-m METADATA_time.txt \
-t time_points \
-f seq.unique.dada2.fasta \
-o mendota_ananke.h5

Running import command gives:

Traceback (most recent call last):
  File "/home/raphenar/h5py/env/bin/ananke", line 11, in <module>
    sys.exit(main())
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/ananke/ananke.py", line 161, in main
    dada2_to_ananke(args.i, args.m, args.t, args.o, args.f, args.multi)
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/ananke/_tabulate.py", line 323, in dada2_to_ananke
    timeseriesdb = TimeSeriesData(timeseriesdata_path)
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/ananke/_database.py", line 78, in __init__
    maxshape=(None,None,), exact=False, fillvalue=-2)	    
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/h5py/_hl/group.py", line 191, in require_dataset
    return self.create_dataset(name, *(shape, dtype), **kwds)
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/h5py/_hl/group.py", line 136, in create_dataset
    dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
  File "/home/raphenar/h5py/env/lib/python3.6/site-packages/h5py/_hl/dataset.py", line 167, in make_new_dset
    dset_id = h5d.create(parent.id, None, tid, sid, dcpl=dcpl)
  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/h5d.pyx", line 80, in h5py.h5d.create
ValueError: Unable to create dataset (no appropriate function for conversion path)

Running ncdump on mendota_ananke.h5 gives:

netcdf mendota_ananke {

// global attributes:
		string :origin_version = "0.3.0" ;

group: genes {
  dimensions:
  	phony_dim_0 = UNLIMITED ; // (1 currently)
  variables:
  	string sequenceclusters(phony_dim_0) ;
  	string sequenceids(phony_dim_0) ;
  	string sequences(phony_dim_0) ;
  	string taxonomy(phony_dim_0) ;
  data:

   sequenceclusters = NIL ;

   sequenceids = NIL ;

   sequences = NIL ;

   taxonomy = NIL ;
  } // group genes

group: timeseries {
  dimensions:
  	phony_dim_1 = UNLIMITED ; // (1 currently)
  variables:
  	int data(phony_dim_1) ;
  	int indices(phony_dim_1) ;
  	int indptr(phony_dim_1) ;
  data:

   data = 0 ;

   indices = 0 ;

   indptr = 0 ;
  } // group timeseries
}

• @mwhall @fmaguire It looks like the code is failing at init method in the TimeSeriesData class because the clusters dataset is not being created (located in the file: https://github.com/beiko-lab/ananke/blob/master/ananke/_database.py)