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.
