我在网上查了方法，把gff文件的mrna行删除，现在又出现了新的问题：
14:31:45.646 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/work/biosoft/picard/picard-3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Sat Dec 16 14:31:45 CST 2023] CreateSequenceDictionary OUTPUT=elepant_grass_genome.dict REFERENCE=elepant_grass_genome.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Sat Dec 16 14:31:45 CST 2023] Executing as majieyu@mgt02 on Linux 3.10.0-1127.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 19.0.1+10-21; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 3.0.0
/share/work/biosoft/picard/picard: line 66: 12030 Killed /share/work/biosoft/java/latest/bin/java -Xms512m -Xmx2g -jar /share/work/biosoft/picard/picard.jar CreateSequenceDictionary "R=elepant_grass_genome.fa" "O=elepant_grass_genome.dict"
awk: cmd. line:1: fatal: cannot open file `elepant_grass_genome.fa.fai' for reading (No such file or directory)
/public/home/majieyu/perl5/ppgwas/reseq/reseq_demo//scripts/index.sh: line 31: [: -gt: unary operator expected
RNN CMD: bwa index elepant_grass_genome.fa
[bwa_index] Pack FASTA... /public/home/majieyu/perl5/ppgwas/reseq/reseq_demo//scripts/index.sh: line 38: 14922 Killed bwa index $fa
gtf file not provide, try get gtf from gff:
RUN CMD: gffread new.gff -T -o new.gtf
build ANNOVAR index
RUN CMD: gtfToGenePred -genePredExt new.gtf unknown_refGene.txt
invalid gffGroup detected on line: chrB6MAKERexon1273930701273934250.000000-.transcript_id "PenpuB60000010.g.72";
GFF/GTF group PenpuB60000010.g.72 on chrB6+, this line is on chrB6-, all group members must be on same seq and strand
RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile elepant_grass_genome.fa unknown_refGene.txt --out unknown_refGeneMrna.fa
NOTICE: Reading region file unknown_refGene.txt ... Done with 4143 regions from 1 chromosomes
/public/home/majieyu/perl5/ppgwas/reseq/reseq_demo//scripts/index.sh: line 56: 18535 Killed retrieve_seq_from_fasta.pl --format refGene --seqfile $fa --outfile unknown_refGeneMrna.fa unknown_refGene.txt
