some error message from BFAST match

[lei]

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.

[nilshomer]

You need more disk space: "No space left on device".

[fenciso]

Hi,
II am new using bfast, I have a question: How can I define the mask values??, in index option.

Thanks

[nilshomer]

Hi,
II am new using bfast, I have a question: How can I define the mask values??, in index option.

Thanks

Welcome! In general, if you have a new question, post to a new thread. Use the "-m" option, and see the appendix in the bfast manual for the recommended settings.

[fenciso]

ok, it works.

Thanks

[xiangwulu]

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 *****

[xiangwulu]

found a solution for my problem.
bfast gives error when align reads contains non a t c g n base.