Converting PE using XSQ_Tools

[beldenwj]

I am trying to convert a .xsq file with PE data using ./convertFromXSQ.sh in XSQ_Tools

I am getting the error message:

LtsIo FAIL: Failed to open runMetadata
Failed to get IsIndexingRun from xsq file -- myfile.xsq

I'm wondering if anyone else has experienced a similar problem?

Thanks.

[colindaven]

I would email this to tech support at lifetech.

I haven't had this problem, but I haven't had PE data yet. Are you sure the XSQ is intact, or does it happen on all files ?

[beldenwj]

It seems to occur with just our PE data. We've been able to convert single reads with no problems.

Thanks for the advice on contacting Lifetech. I let you know what I find out.

[beldenwj]

I'm not sure if anyone cares but the problem arose somewhere in the data transfer. Somehow the RunMetaData was lost which I determine by examining the .xsq file in HDF5view.

[jeffhsu3]

Are F3 and F5 portions kept in the same xsq file?
Also out of curiosity did the hashes checkout in the failed file?

[beldenwj]

Jeffhsu3

The F3 and F5 files were compressed in the same xsq file. It turned out that our core facility was having trouble converting the data into an seq file and the RunMetaData was missing. When they recompiled the data we had no problems.

I hope that answered your questions.