parallel hanging when used with pipe

[juncus]

I was using parallel to do blast searches on a large number of
biological sequences.

cat sequences.fasta | parallel --block 2k --recstart '>' --pipe -j 30
"blastn -db nt -task blastn -evalue 0.00001 \
  -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend
sstart send evalue bitscore ppos' \
  -max_target_seqs 5 -query -" > results.txt

It hung after a few hours.  Only about 40% of the input file had been
processed.  No blastn processes were running, and the parallel process
was in sleep (S) state.

I killed the parallel process and got this message:

parallel: SIGTERM received. No new jobs will be started.
parallel: Waiting for these 0 jobs to finish. Send SIGTERM again to stop now.


This message seems somehow pathological.  Parallel is waiting for zero
jobs to finish.  This must surely be connected with why it was hanging
(it didn't get the message that jobs were done, so it didn't spawn new
jobs.)

This is not happening all the time, so difficult for me to diagnose.  Any clues?

Thanks very much,
Owen


$ parallel --version
GNU parallel 20130222
Copyright (C) 2007,2008,2009,2010,2011,2012,2013 Ole Tange and Free
Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
GNU parallel comes with no warranty.

Web site: http://www.gnu.org/software/parallel

When using GNU Parallel for a publication please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.