how to obtain subreads from *.bax.h5 files

Question

[wes]

I had downloaded RSII data from NCBI which consists of three *.bax.h5.1 files and one bas.h5.1 file.

Next, I would like to obtain subreads file using pbh5tools.

By referring to guideline below, the input is bas.h5 file but there is error. May I know if the cmd below is correct? or should I use baxh5.1 as input file which I tried as well (shown below) but error too.

http://lira.no-ip.org:8080/doc/python-pbh5tools/html/#installation

bash5tools.py --outFilePrefix m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.subreads --readType subreads --outType fastq m150803_212153_42216_c100858342550000001823192601241650_s1_p0.bas.h5.1

Traceback (most recent call last):
File "/home/cbr01/anaconda3/envs/py2/bin/bash5tools.py", line 166, in
sys.exit(BasH5ToolsRunner().start())
File "/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/util/ToolRunner.py", line 85, in start
return self.run()
File "/home/cbr01/anaconda3/envs/py2/bin/bash5tools.py", line 121, in run
inBasH5 = BasH5Reader(self.args.inFile)
File "/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py", line 660, in init
for fn in self.file["/MultiPart/Parts"] ]
File "/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py", line 304, in init
raise IOError("Invalid or nonexistent bax/bas file %s" % filename)
IOError: Invalid or nonexistent bax/bas file /media/cbr01/analysis/WEE/DNASeq/SRX2718652/m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.bax.h5

bash5tools.py --outFilePrefix m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.subreads --readType subreads --outType fastq m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.bax.h5.1
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:273: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
numEvent = h5Group["ZMW/NumEvent"].value
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:274: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
holeNumber = h5Group["ZMW/HoleNumber"].value
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:349: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
holeNumbers = self._mainBasecallsGroup["ZMW/HoleNumber"].value
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:356: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
fh["/PulseData/Regions"].value)
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:379: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
holeStatus = self._mainBasecallsGroup["ZMW/HoleStatus"].value
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:388: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
(self._mainBasecallsGroup["ZMW/NumEvent"].value > 0) &
/home/cbr01/anaconda3/envs/py2/lib/python2.7/site-packages/pbcore/io/BasH5IO.py:565: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
self.__metricCache[name] = self._mainBasecallsGroup[k].value

[GenoMax]

usage: bash5tools.py [-h] [--verbose] [--version] [--profile] [--debug]
                     [--outFilePrefix OUTFILEPREFIX]
                     [--readType {ccs,subreads,unrolled}] [--outType OUTTYPE]
                     [--minLength MINLENGTH] [--minReadScore MINREADSCORE]
                     [--minPasses MINPASSES]
                     input.bas.h5

Tool for extracting data from .bas.h5 files

positional arguments:
  input.bas.h5          input .bas.h5 filename

You need to use the bas file.

IOError: Invalid or nonexistent bax/bas file /media/cbr01/analysis/WEE/DNASeq/SRX2718652/m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.bax.h5

There is also an error about the bax file. Are these files in the same directory? Did you download them as binary files?

[wes]

Dear Genomax

I download the original format of PacBio data- three bax.h5.1 and bas.h5.1 file directly from this link under data access https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5428623 May I know how to download as binary file?

Yes, they are under the same directory (base) cbr01@cbr01-Precision-T7600:/media/cbr01/analysis/WEE/DNASeq/SRX2718652$ ls m150803_212153_42216_c100858342550000001823192601241650_s1_p0.1.bax.h5.1 m150803_212153_42216_c100858342550000001823192601241650_s1_p0.2.bax.h5.1 m150803_212153_42216_c100858342550000001823192601241650_s1_p0.3.bax.h5.1 m150803_212153_42216_c100858342550000001823192601241650_s1_p0.bas.h5.1 m150803_212153_42216_c100858342550000001823192601241650_s1_p0.metadata.xml