Question: an error occurring after run the annovar commad ,
0
gravatar for 543541656
4 months ago by
54354165620
54354165620 wrote:
perl annotate_variation.pl --geneanno --dbtype refGene --buildver msuv7 --outfile /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/msu_result /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/candidatesnp_final.avinput msudb/

NOTICE: Output files are written to /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/msu_result.variant_function, /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/msu_result.exonic_variant_function
NOTICE: Reading gene annotation from msudb/msuv7_refGene.txt ... Done with 66338 transcripts (including 0 without coding sequence annotation) for 55986 unique genes
NOTICE: Processing next batch with 267 unique variants in 267 input lines
NOTICE: Variants with invalid input format are written to /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/msu_result.invalid_input

after running the 'perl annotate_variation.pl' command,why the message do not display read fasta like this 'NOTICE: Reading FASTA sequences from ricedb/gcf_refGeneMrna.fa ... Done with 52 sequences'

snp annotation • 106 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe66k • written 4 months ago by 54354165620
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