pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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#001: H5Gint.c line 833 in H5G_iterate(): unable to register group #13 #198

Closed antonkulaga closed 6 years ago

antonkulaga commented 6 years ago

I cannot figure out if it is wassabi or sleuth bug (opened also an issue in wasabi https://github.com/COMBINE-lab/wasabi/issues/13 ) When I open abudance.h5 file with sleuth ( the file is at http://agingkills.westeurope.cloudapp.azure.com/pipelines/samples/GSE36041/GSM879796/ ), I get the following error:

reading in kallisto results
dropping unused factor levels
.HDF5-DIAG: Error detected in HDF5 (1.8.19) thread 0:
  #000: H5L.c line 1181 in H5Literate(): link iteration failed
    major: Symbol table
    minor: Iteration failed
  #001: H5Gint.c line 833 in H5G_iterate(): unable to register group
    major: Object atom
    minor: Unable to register new atom
  #002: H5I.c line 880 in H5I_register(): invalid type
    major: Object atom
    minor: Unable to find ID group information
Error: C stack usage  7972356 is too close to the limit
In addition: Warning message:

I use the sleuth version published at bioconductor 3.7 (Sleuth 0.30.0)

antonkulaga commented 6 years ago

Looks like it was wasabi issue, closing it