Question: (Closed) Minia 2.0.3 binary spits out lots of HDF5 errors if -out-dir doesn't exit
0
gravatar for Torst
3.3 years ago by
Torst900
Australia
Torst900 wrote:

This fails:  rm -fr foo && ./minia -in ~/tmp/R1.fastq -out-dir foo

This works: mkdir foo && ./minia -in ~/tmp/R1.fastq -out-dir foo

If 'foo' doesn't exist it spits LOTS of messages like this:

HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
  #000: /home/vagrant/gatb-tools/gatb-tools/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5F.c line 1500 in H5Fcreate(): unable to create file
    major: File accessibilty
    minor: Unable to open file
  #001: /home/vagrant/gatb-tools/gatb-tools/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5F.c line 1282 in H5F_open(): unable to open file: time = Mon Dec  7 12:46:57 2015
, name = 'foo/R1.h5', tent_flags = 13
    major: File accessibilty
    minor: Unable to open file
  #002: /home/vagrant/gatb-tools/gatb-tools/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5FD.c line 987 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: /home/vagrant/gatb-tools/gatb-tools/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDsec2.c line 343 in H5FD_sec2_open(): unable to open file: name = 'foo/R1.h5', errno = 2, error message = 'No such file or directory', flags = 13, o_flags = 242
    major: File accessibilty
    minor: Unable to open file

 

minia • 962 views
ADD COMMENTlink written 3.3 years ago by Torst900

What's the question ? You already know how to solve the problem. If you want to create a file in a directory, you must create this directory first. This is a general rule, not specific to HDF5.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche18k

Hello Torst!

This post, while of potential interest, is not a question.  

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Sean Davis25k

Hi Torsten! Thanks for letting us know. I've just fixed it; it will be available in the next release. Stay tuned for Minia 3 :)

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Rayan Chikhi1.4k
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