include info on how many seuqences were downloaded from GISAID

roblanf · Jun 14, 2020 · b64af4b · b64af4b
1 parent a51da9a
commit b64af4b
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/scripts/global_tree_gisaid.sh b/scripts/global_tree_gisaid.sh
@@ -76,6 +76,9 @@ esl-alimask --gapthresh 0.5 --informat afa --outformat afa --dna -o $outputfasta
 
 rm tmp.aln
 
+echo "sequences downloaded from GISAID" >> alignments.log
+echo grep ">" $inuptfasta | wc -l >> alignments.log
+echo "//"
 echo "alignment stats of global alignment" >> alignments.log
 esl-alistat $aln_global >> alignments.log
 echo "alignment stats of global alignment after masking sites" >> alignments.log