line 2 is too short: the value for --reference-column is 2
can't find feature with name "mcm4-td" at line 3 - skipping
line 8 is too short: the value for --reference-column is 2
can't find feature with name "mcl1-3(mcl1-3xHA)" at line 9 - skipping
can't find feature with name "mcl1-4(mcl1-3xFLAG)" at line 10 - skipping
can't find feature with name "atp1-2313" at line 12 - skipping
can't find feature with name "tti2-CKO" at line 16 - skipping
can't find feature with name "cnd2-TEV" at line 28 - skipping
can't find feature with name "alp7-5A(S50A,S51A,T100A,T116A,T131A)" at line 94 - skipping
can't find feature with name "alp7-5A(K341,Y344,R346,K347,Y348)" at line 95 - skipping