line 5 is too short: the value for --reference-column is 2
can't find feature with name "mcl1-3(mcl1-3xHA)" at line 6 - skipping
can't find feature with name "mcl1-4(mcl1-3xFLAG)" at line 7 - skipping
can't find feature with name "atp1-2313" at line 9 - skipping
can't find feature with name "tti2-CKO" at line 13 - skipping
can't find feature with name "cnd2-TEV" at line 25 - skipping
can't find feature with name "alp7-5A(S50A,S51A,T100A,T116A,T131A)" at line 91 - skipping
can't find feature with name "alp7-5A(K341,Y344,R346,K347,Y348)" at line 92 - skipping