big tests oom

Author: mlin

test/genomicsqlite_big_tests.wdl

@@ -128,11 +128,9 @@ task test_sam {
         # page compression stats
         time sqlite3 "~{dbname}" "SELECT meta1, count(*), avg(length(data)) FROM nested_vfs_zstd_pages GROUP BY meta1" >&2
 
-        # add a QNAME-sorted seqs table
+        # add a QNAME-sorted seqs table. TODO: write it into a separate attached db
         chmod +x /usr/lib/python3.8/genomicsqlite.py
-        time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "PRAGMA journal_mode=off; PRAGMA synchronous=off; PRAGMA cache_size=-4194304; CREATE TABLE reads_seqs_by_qname AS SELECT * from reads_seqs NOT INDEXED ORDER BY qname"
-        >&2 ls -l "~{dbname}"
-        time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "PRAGMA journal_mode=off; PRAGMA synchronous=off; DROP TABLE reads_seqs_by_qname"
+        time /usr/lib/python3.8/genomicsqlite.py "~{dbname}" "PRAGMA journal_mode=off; PRAGMA synchronous=off; CREATE TABLE reads_seqs_by_qname AS SELECT * from reads_seqs NOT INDEXED ORDER BY qname"
         >&2 ls -l "~{dbname}"
     >>>