gravatar for manozawa439

2 hours ago by

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)
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