Error in rhdf5::h5ls(fname) : HDF5. Object header. Can't open object.

[mbartl13]

Hi all- having an issue getting the sleuth object set:

Upload metadata

metadata <- read.delim("/dcl02/leased/giffin/SINV_RNAseq/fastq/metadata.txt")

metadata <- read.table(dcl02/leased/giffin/SINV_RNAseq/fastq/'metadata.txt', sep='\t', header=TRUE, stringsAsFactors = FALSE)

metadata <- dplyr::select(metadata, c('SampleName', 'Time', 'Condition', 'Replicate'))

rename SampleName to sample

metadata <- dplyr::rename(metadata, sample = SampleName) head(metadata)

set path to kallisto outputs

metadata <- dplyr::mutate(metadata, path = file.path('.', 'trim', 'trimmed', 'kallisto_out', sample, 'abundance.h5'))

Associating transcripts to genes

mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl", host = "dec2015.archive.ensembl.org") ttg <- getBM( attributes = c("ensembl_transcript_id", "transcript_version", "ensembl_gene_id", "external_gene_name", "description", "transcript_biotype"), mart = mart) ttg <- dplyr::rename(ttg, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name) ttg <- dplyr::select(ttg, c('target_id', 'ens_gene', 'ext_gene')) head(ttg)

create sleuth object

so <- sleuth_prep(metadata, target_mapping = ttg, aggregation_column = 'ens_gene', extra_bootstrap_summary = TRUE) dropping unused factor levels ....................Error in rhdf5::h5ls(fname) : HDF5. Object header. Can't open object.

Thanks in advance! Maggie