try different approach to solve cut: write error: Broken pipe

metaDMG-dev · May 6, 2024 · 8d8e478 · 8d8e478
1 parent de17b9f
commit 8d8e478
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/test/testAll.sh b/test/testAll.sh
@@ -79,7 +79,16 @@ echo "Running test of output/test_dfit_local.dfit.gz by gzip -t  output/test_dfi
 gzip -t  output/test_dfit_local.dfit.gz
 echo -ne "Return value of test $?\nWill now run gunzip -c output/test_dfit_local.dfit.gz|wc -c\n"
  gunzip -c output/test_dfit_local.dfit.gz|wc -c
-zcat output/test_dfit_local.dfit.gz | cut -f 1-6,8- | head -n 10 | numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
+
+
+zcat output/test_dfit_local.dfit.gz > tmp.txt
+cat tmp.txt | head -n 10 > tmp2.txt
+rm tmp.txt
+cut -f 1-6,8- tmp2.txt| numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
+rm tmp2.txt
+#zcat output/test_dfit_local.dfit.gz | head -n 10|cut -f 1-6,8- | numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
+#exit 0
+
 
 echo "Running dfit local (10 threaded)"
 CMD="${PRG} dfit output/test_lca.bdamage.gz --threads 10 --names data/names.dmp.gz --nodes data/nodes.dmp.gz --showfits 2 --nopt 2 --nbootstrap 2 --seed 12345 --lib ds --out output/test_dfit_local_10threads"