This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Minia 2.0.3 binary spits out lots of HDF5 errors if -out-dir doesn't exit

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
• 1,799 views • link
updated by Ram Ram • written by Torst Torst

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.

• 0 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

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!

• 0 views • link
updated by Ram Ram • written by Sean Davis Sean Davis

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 :)

• 1 views • link
written by Rayan Chikhi Rayan Chikhi

0 answers

No answers yet.

Log in to answer this question.

More posts like this