MutSig preprocessing step: categ and effect

The following is first few lines of mutation input, which was created during MutSig pre-processing step. As you can see, most of "categ" is classified as "null+indel", and in fact, "null+indel" constitutes the majority of mutations I am querying.

patient gene Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change effect chr start ref_allele categ
G1_04 FAM35A 54537 broad.mit.edu 37 10 88912397 88912397 + Frame_Shift_Del DEL C - - g.chr10:88912397delC uc001kei.3 + 3 1400 c.1286delC c.(1285-1287)ACAfs p.T429fs null 10 88912397 C null+indel
G1_04 MINPP1 9562 broad.mit.edu 37 10 89265006 89265007 + Frame_Shift_Ins INS - G G g.chr10:89265006_89265007insG uc001keu.2 + 1 784_785 c.334_335insG c.(334-336)CGCfs p.R112fs null 10 89265006 - null+indel
G1_04 MDN1 23195 broad.mit.edu 37 6 90402185 90402185 + Nonsense_Mutation SNP G A A g.chr6:90402185G>A uc003pnn.1 - 63 10680 c.10564C>T c.(10564-10566)CAG>TAG p.Q3522* null 6 90402185 G null+indel
G1_04 KIAA0664P3 100132341 broad.mit.edu 37 16 31718222 31718222 + RNA DEL G - - g.chr16:31718222delG uc002eck.3 + 9 c.1253delG noncoding 16 31718222 G ---
G1_04 PLA2G1B 5319 broad.mit.edu 37 12 120763680 120763681 + Frame_Shift_Ins INS - G G rs145575269 g.chr12:120763680_120763681insG uc001tyd.2 - 2 213_214 c.177_178insC c.(175-180)CCCGTGfs p.P59fs null 12 120763680 - null+indel
G1_04 FHDC1 85462 broad.mit.edu 37 4 153896047 153896048 + Frame_Shift_Ins INS - C C g.chr4:153896047_153896048insC uc003inf.2 + 11 1679_1680 c.1604_1605insC c.(1603-1605)AACfs p.N535fs null 4 153896047 - null+indel
G1_04 MAP3K9 4293 broad.mit.edu 37 14 71199679 71199679 + Missense_Mutation SNP G A A g.chr14:71199679G>A uc001xmm.2 - 11 2407 c.2407C>T c.(2407-2409)CGT>TGT p.R803C nonsilent 14 71199679 G *CpG->T

More than 90% of mutations are classified as "null+indel" mutations. As a result, "effect" field becomes "null".

There is no noticeable error/warning message during preprocessing step. However, I am getting the following warning message probably due to incomplete preprocessing of inputs. I am using the same reference files listed on MutSig website.

NOTE: 256/5027 gene names could not be mapped to coverage information. Excluding them.
NOTE: 182/7946 mutations were outside the category set. Excluding them.

Warning: silent and nonsilent rates are too different.
WARNING: coding and noncoding rates are too different

Please help me if I am doing something wrong. Thank you.

-Ryan