From 14739780f1978e23b55d13910e5f8f5947de16bb Mon Sep 17 00:00:00 2001 From: meesters Date: Wed, 21 Aug 2019 12:34:42 +0200 Subject: [PATCH] reduced the number of split files for the default --- blast/parallel_BLAST/LA_Wrapper | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/blast/parallel_BLAST/LA_Wrapper b/blast/parallel_BLAST/LA_Wrapper index 6f5d924..3bb07c4 100755 --- a/blast/parallel_BLAST/LA_Wrapper +++ b/blast/parallel_BLAST/LA_Wrapper @@ -175,10 +175,14 @@ credits() { echo "The original implementation (2013/2014) was written by Christoph Martin (ZDV, UNIX group)" echo "Benjamin Rieger (Institut für Molekulargenetik) contributed a perl implementation" - echo "of a format conform splitting of FASTA files." + echo "of a format conform splitting of FASTA files, which is not used, anymore." echo "The original implemenation was a LSF chain job. It was eventually adopted and maintained by" echo "Christian Meesters (ZDV, HPC group) from 2017 onwards." echo + echo "I am particularly grateful for their feedback to:" + echo "- Lukas Hellman (AG Hankeln)" + echo "- Benjamin Rieger (NGS Facility)" + echo echo "History of the re-implementation:" echo "- v0.1 -- 27. Sep. 2017 -- release of the re-implementation for SLURM supporting the" echo " ability to compute accross nodes." @@ -201,7 +205,7 @@ credits() echo "- v0.3.2 -- 16. Jan. 2019 -- hot fix for new ramdisk and slurmstepd support" echo "- v0.4 -- 06. Mar. 2019 -- refactored version:" echo " - executables now pluggable" - echo "- v0.5 -- 17. Aug. 2019 -- fix: parser did not work for '--mem'-arg properly" + echo "- v0.5 -- 21. Aug. 2019 -- fix: parser did not work for '--mem'-arg properly" echo " update: - clearer UI" echo " - better default memory settings" echo " - faster stage-in for reference data" @@ -494,10 +498,10 @@ if [ $_arg_splitup_per_queryfile -ne 0 ]; then # the user thinks differently? error "There would be more than '$nsplits' files in scratch." exit 1 elif [ $nsplits -gt 15000 ]; then - warning "There will be '$nsplits' files in scratch." + warning "There will be '$nsplits' files in scratch -- resulting in poor performance." fi else # infer the value - _arg_splitup_per_queryfile=$((nentries / 10000)) + _arg_splitup_per_queryfile=$((nentries / 5000)) fi # default values, see: -- GitLab