log changes

wGRR

@@ -226,21 +226,19 @@ if [[ -f $OUT.m8 ]] ; then
 	echo "[INFO]      --  Using existing MMseqs output file $OUT.m8"
 else
 	MIDENT=$($AWKEXE '!/^>/{a[$0]++}END{for(i in a){if(a[i]>m){m=a[i]}}print m}' $PRT)
+	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 	if [[ $((MIDENT*2)) -gt "$MMS_DEF_MAX_SEQS" ]] ; then
 		MMS_MAX_SEQ_PARAM=($(echo $((MIDENT*2)) | awk '{c=substr($1,2);gsub(/[0-9]/,0,c);print "--max-seqs "substr($1,1,1)+1""c}'))
 		echo "[INFO]      --  Setting MMseqs parameter $MMS_MAX_SEQ_PARAM"
 	fi
-
 	if [[ $BATCHFLAG == 1 ]] ; then
 		printf "%-10s  --  %s\n" "[INFO]" "Submitting MMseqs search to Maestro"
-		printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 		JID=$(sbatch --wait --parsable -o "$OUT".mmseqs.log -p $PARTITION -c $THREADS -J "wGRR_MMSeqs" --wrap="$MMSEQS easy-search $PRT $PRT ${OUT}.m8 ${tmp} --threads $THREADS --format-output \"query,target,qcov,tcov,fident,evalue,bits\" --add-self-matches $MMS_MAX_SEQ_PARAM")
 		PQT=$(sacct -X -j $JID -o Reserved -n | awk '{n=split($1,a,"-");if(n>1){t=t+a[1]*86400};split(a[n],b,":");t=t+b[1]*3600+b[2]*60+b[3];print t}')
 		echo "[INFO]      --  The job $JID has been "$(textifyDuration $PQT) "in queue"
 		QT=$((QT+PQT))
 	else
 		printf "%-10s  --  %s\n" "[INFO]" "Running MMseqs search"
-		printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 		$MMSEQS easy-search $PRT $PRT $OUT.m8 $tmp --threads $THREADS --format-output "query,target,qcov,tcov,fident,evalue,bits" --add-self-matches $MMS_MAX_SEQ_PARAM > $OUT.mmseqs.search.log
 	fi
 fi
@@ -254,8 +252,8 @@ duration=$SECONDS
 if [[ -f $OUT.allpairs.txt ]] ; then
 	echo "[INFO]      --  Using existing file $OUT.allpairs.txt"
 else
-	printf "%-10s  --  %s\n" "[INFO]" "Writing genomes pairs"
 	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
+	printf "%-10s  --  %s\n" "[INFO]" "Writing genomes pairs"
 	$AWKEXE 'BEGIN{x=1}/^>/{g=substr($1,2);gsub(/_[0-9]+$/,"",g);if(FNR==1){a[x]=g;++x;currg=g;next}if(g!=currg){a[x]=g;x++;currg=g}}END{i=0;while(++i in a){j=i;while(++j in a){print a[i]"\t"a[j]}}}' $PRT > $OUT.allpairs.txt
 	printf "%-10s  --  %s\n" "[INFO]" "$(wc -l $OUT.allpairs.txt | awk '{print $1}') pairs written"
 fi
@@ -292,13 +290,13 @@ if [[ $BATCHFLAG == 0 ]] ; then
 		printf "\n"
 	fi
 else
+	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 	REQMEM=""
 	echo "[INFO]      --  Estimating required memory"
 	M1=$(awk -f wGRR.awk -v MINP=1 -v MAXP=10 -v OUT=$OUT -v MEM=1 $OUT.allpairs.txt $PRT $OUT.m8)
 	REQMEM=$(bc -l <<< $(numfmt --from=iec $M1)*($ARRAYSIZE/10) | numfmt --to=iec | awk '{U=$0;gsub(/[^A-Za-z]/,"",U);V=$0;gsub(/[A-Za-z]+$/,"",V);split(V,a,".");n=split(a[1],b,"");c=b[1]+1;i=1;while(++i<=n){c=c"0"}print c""U}')
 	echo "[INFO]      --  $REQMEM per job required"
 	duration=$SECONDS
-	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 	echo "[INFO]      --  Submitting $NJOBS jobs for wGRR calculation"
 	if [[ $MAXJOBS -gt 0 ]] && [[ $MAXJOBS -lt $NJOBS ]] ; then
 		echo "[INFO]      --  Limiting the number of simultaneous jobs to $MAXJOBS"
@@ -315,8 +313,8 @@ else
 fi
 
 duration=$SECONDS
-printf "%-10s  --  %s\n" "[INFO]" "Sorting results"
 printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
+printf "%-10s  --  %s\n" "[INFO]" "Sorting results"
 sort -m "$tmp"/$OUT.wgrr_part.* | sort -u -k1,1V -k2,2V | $AWKEXE 'BEGIN{print "GenomeA\tGenomeB\twGRR1\tCommon1\tRealLengthA\tRealLengthB\twGRR2\tCommon2\tEffectiveLength1A\tEffectiveLength1B\twGRR3\tCommon3\tEffectiveLength2A\tEffectiveLength2B"}1' > $OUT.wgrr.txt
 
 if [[ ! -f "$OUT".wgrr.txt ]] ; then