VCF to HDF5 Error

[PaulinaUrbana]

Hi, I am getting error when converting VCF files downloaded from 1000G using snp2h5 by chromosome. I was wondering whether this has something to do with my input or the version of HDF5 I'm using. If you could please give any suggestions to why this is happening, it would be really helpful. Thank you!

Script:

$WASP/snp2h5/snp2h5 --chrom $HOME/WASP/mapping/genome/b37.chrom.sizes.txt\
        --format vcf \
        --haplotype $OUTPUT_DIR/haplotypes.h5 \
        --snp_index $OUTPUT_DIR/snp_index.h5 \
        --snp_tab   $OUTPUT_DIR/snp_tab.h5 \
        $INPUT

Error:

HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 22946543359808:
  #000: H5Dio.c line 315 in H5Dwrite(): can't prepare for writing data
    major: Dataset
    minor: Write failed
  #001: H5Dio.c line 388 in H5D__pre_write(): can't write data
    major: Dataset
    minor: Write failed
  #002: H5Dio.c line 829 in H5D__write(): can't write data
    major: Dataset
    minor: Write failed
  #003: H5Dchunk.c line 2438 in H5D__chunk_write(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #004: H5Dchunk.c line 3659 in H5D__chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #005: H5Z.c line 1279 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #006: H5Zdeflate.c line 123 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
ERROR: snptab.c:126: failed to write record 249 for SNP '.' to SNP table

Error for one chromosome looked slightly different:

HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 22943714842432:
  #000: H5F.c line 445 in H5Fcreate(): unable to create file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 1604 in H5F_open(): unable to read superblock
    major: File accessibilty
    minor: Read failed
  #002: H5Fsuper.c line 630 in H5F__super_read(): truncated file: eof = 96, sblock->base_addr = 0, stored_eof = 2048
    major: File accessibilty
    minor: File has been truncated
ERROR: snp2h5.c:358: could not create file '/rds/general/user/pu1918/ephemeral/WASP/results/genotypes/snp_index.h5'