The problem about HDF5-DIAG

[xingjianfeng100]

Hi @fanggang
When I use
"fracInsilico <- smrterSyntheticControl( path="aligned_reads_1.cmp.h5" , sitesInfo_interest=natVATB , split_chunk_num=2000 , cores=20 , type = 'callMod' , coverage_per_molecule=3 , number_of_molecule=5 , coverage_thres=15 , score_thres=0) resInsilico <- do.call( rbind , fracInsilico ) quantile( subset(resInsilico,ipdRatio>4.5)$frac , seq(0,1,0.1) , na.rm=T ) "
to Fraction call at single molecule level, I get the following error message
"HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
#000: H5D.c line 294 in H5Dopen2(): unable to open dataset
major: Dataset
minor: Can't open object
#1: H5Dint.c line 1314 in H5D__open_name(): not found
major: Dataset
minor: Object not found
#2: H5Gloc.c line 428 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#3: H5Gtraverse.c line 867 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#4: H5Gtraverse.c line 639 in H5G_traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#005: H5Gloc.c line 383 in H5G_loc_find_cb(): object 'IPD' doesn't exist
major: Symbol table
minor: Object not found
Error in .local(h5Obj, datasetName, ...) :
Dataset: /ref000001/m130809_050409_42175_c100560932550000001823089712221321_s1_p0/IPD cannot be opened."
or
"HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
#000: H5F.c line 511 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#1: H5Fint.c line 1519 in H5F_open(): unable to lock the file
major: File accessibilty
minor: Unable to open file
#2: H5FD.c line 1650 in H5FD_lock(): driver lock request failed
major: Virtual File Layer
minor: Can't update object
#3: H5FDsec2.c line 939 in H5FD_sec2_lock(): file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override), errno = 38, error message = 'Function not implemented'
major: File accessibilty
minor: Bad file ID accessed
Error in .local(.Object, ...) :
Problem opening file: aligned_reads_1.cmp.h5"
Can you give me some indication as to what may be wrong?
thanks!

[zhushijia]

Hi @xingjianfeng100,

Thank you for your question. Apologies for the delay. We did not experience this problem before with our own data or others’ data we analyzed. We also tried to search, but did not get an answer. If it is possible to share your data, or part of it, we will try the best to help. Of course, the data will not be used for any other purpose.

Best