HDF5-DIAG: Error in using dsk

Question

[manozawa439]

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)
------------------------------------------------------------

[manozawa439]

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.

[GenoMax]

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.

Answer 1

[claire.lemaitre]

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

[GenoMax]

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.

[claire.lemaitre]

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.

[GenoMax]

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

[Rayan Chikhi]

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.

[claire.lemaitre]

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.