[Swift-user] exceptions in running many data files
Wenjun Wu
wwj at ci.uchicago.edu
Wed Jan 21 13:50:05 CST 2009
Hello,
I often get the following exception while running thousands of files:
Progress:
java.io.IOException: Bad file descriptor
at java.io.FileInputStream.available(Native Method)
at
java.io.BufferedInputStream.available(BufferedInputStream.java:337)
at org.griphyn.vdl.karajan.InHook.run(InHook.java:37)
at java.lang.Thread.run(Thread.java:534)
My workfow script looks like this:
seqfile trunks[] <filesys_mapper;location="./data", prefix=@arg("orig"),
suffix=".fas">;
foreach file in trunks {
seqfile outvid <regexp_mapper;source=@file, match="(.*)fas",
transform="\\1out">;
outvid = runAnalysis(file);
}
Could anyone give any suggestion about how to fix such an exception?
Thanks,
Wenjun
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