[Swift-user] exceptions in running many data files

[Wenjun Wu]

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