found a solution for my problem.
bfast gives error when align reads contains non a t c g n base.
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had similar error too, like the following:
In function "AlignedEndRead": Fatal Error[ReadFileError]. Variable/Value: a->reads, a->qual, and a->numEntries.
Message: Could not read from file.
The file stream error was:: Success
***** Exiting due to errors *****
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Originally posted by fenciso View PostHi,
II am new using bfast, I have a question: How can I define the mask values??, in index option.
Thanks
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Hi,
II am new using bfast, I have a question: How can I define the mask values??, in index option.
Thanks
Leave a comment:
-
some error message from BFAST match
hi,
I got some error message when I use BFAST for solid data mapping:
error 1:
In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write m->readLength, m->qualLength, m->read, m->qual, m->maxReached, and m->numEntries.
The file stream error was:: No space left on device
***** Exiting due to errors *****
Does it mean I don't have enough memory or space to run it? But I run it on a cluster, it should have enough memory or space.
error 2:
In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write masks[i].
The file stream error was:: No space left on device
***** Exiting due to errors *****
error 3:
************************************************************
Searching for main indexes...
************************************************************
In function "GetIndexFileNames": Fatal Error[OutOfRange]. Variable/Value: /icgc/lsdf/mb/analysis_final/reference/bfastCS/hg19.fa.cs.
Message: Could not find any indexes with the given prefix.
***** Exiting due to errors *****
For this error, I do have indexes there. Sometimes it can find them, sometimes it reports this error. So I don't understand why.Tags: None
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