Off topic:Minia 2.0.3 binary spits out lots of HDF5 errors if -out-dir doesn't exit
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8.4 years ago
Torst ▴ 980

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 • 1.6k views
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