Question: HDF5-DIAG: Error in using dsk
0
gravatar for manozawa439
12 days ago by
manozawa4390 wrote:

Hi,

When I use dsk with the following command, I got the error below.

dsk -file /home2/nozawa/montium_ssg/DNAseq/kmer/Q25L50/k-awa31F_list.txt \
    -storage-type file \
    -max-memory 100000 \
    -kmer-size 31 \
    -out-dir /home2/nozawa/montium_ssg/DNAseq/kmer/Q25L50 \
    -out k-awa31F_kmer.txt

the content of k-awa31F_list.txt is as follows.

/home2/nozawa/montium_ssg/DNAseq/Fastq/Q25L50/lac_IR-M08F_R1_cutadapt.fastq.trimmed.paired
/home2/nozawa/montium_ssg/DNAseq/Fastq/Q25L50/lac_IR-M08F_R2_cutadapt.fastq.trimmed.paired
/home2/nozawa/montium_ssg/DNAseq/Fastq/Q25L50/lac_IR-M08F_R1_cutadapt.fastq.trimmed.single

Could you please give me some suggestions?

Best regards, Fumi

-----------------------------error message from here-------------------------------

HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c line 425 in H5Aopen(): unable to load attribute info from object header for attribute: 'version'
    major: Attribute
    minor: Can't open object
  #001: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5Aint.c line 433 in H5A__open(): unable to load attribute info from object header for attribute: 'version'
    major: Attribute
    minor: Can't open object
  #002: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5Oattribute.c line 515 in H5O__attr_open_by_name(): can't locate attribute: 'version'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c line 704 in H5Aget_space(): not an attribute
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5S.c line 1013 in H5Sget_simple_extent_dims(): not a dataspace
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: /scratchdir/builds/workspace/gatb-dsk/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c line 662 in H5Aread(): not an attribute
    major: Invalid arguments to routine
    minor: Inappropriate type
EXCEPTION: Unable to open bank '/home2/nozawa/montium_ssg/DNAseq/Fastq/Q25L50/la' (if it is a list of files, perhaps some of the files inside don't exist)
------------------------------------------------------------
gatb • 92 views
ADD COMMENTlink modified 12 days ago by claire.lemaitre120 • written 12 days ago by manozawa4390

Hi,

Additional information. I am using Ubuntu20.04LTS and downloaded dsk-v2.3.3-bin-Linux.tar.gz from https://github.com/GATB/dsk/releases.

ADD REPLYlink written 12 days ago by manozawa4390

Just a speculation but I don't know if dsk is expecting the fastq file names to actually end in .fastq. May want to try that out.

ADD REPLYlink written 12 days ago by GenoMax96k
1
gravatar for claire.lemaitre
12 days ago by
France
claire.lemaitre120 wrote:

Hi,

The file extension should not be a problem, as long as it is the same in the file and in the input txt file (ie if your file name ends with .fastq, it must be named also with .fastq in the input txt file).

Did you generate your txt file on windows ? If so, you can try to reformat it in unix format with :

dos2unix input_file.txt

Regards, Claire

ADD COMMENTlink written 12 days ago by claire.lemaitre120

Do you have first hand experience with this program?

The file extension should not be a problem, as long as it is the same in the file and in the input txt file (ie if your file name ends with .fastq, it must be named also with .fastq in the input txt file).

How is that not a problem if the program requires the file names to end in .fastq? As you saw from the example in original question, OP's file names do not have that extension.

ADD REPLYlink written 11 days ago by GenoMax96k

DSK does not require any specific extension. It worked for me with files without the .fastq or .fasta extension, and DSK recognizes the format from the content of the file.

ADD REPLYlink written 11 days ago by claire.lemaitre120

Thanks for the confirmation. Original poster will need to respond to provide an update then.

ADD REPLYlink written 11 days ago by GenoMax96k

Thanks Claire! Yes, agreed, and please let us know if DSK worked for you with a .txt file pointing to different files (possibly without underscores..), or not.

ADD REPLYlink written 11 days ago by Rayan Chikhi1.5k
1

Yes it worked with the following txt file for instance :

A_R1
AR2

with the first file being in fastq format and the second in fasta, both without any extension in my current directory.

ADD REPLYlink written 11 days ago by claire.lemaitre120
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