[majieyu@mgt02 ref]$ singularity exec /public/home/majieyu/perl5/gwas-sif/reseq.sif sh $scriptdir/index.sh elepant_grass_genome.fa elepant_grass_genomenew.gff

INFO:    Converting SIF file to temporary sandbox...

REF: elepant_grass_genome.fa

GFF: elepant_grass_genomenew.gff

GTF:

mv: cannot stat ‘elepant_grass_genomenew.gff’: No such file or directory

cat: elepant_grass_genomenew.gff.bak: No such file or directory

build Index  start:

RNN CMD:samtools faidx elepant_grass_genome.fa

/public/home/majieyu/perl5/ppgwas/reseq/reseq_demo//scripts/index.sh: line 22: 18444 Killed                  samtools faidx $fa

RNN CMD: picard CreateSequenceDictionary R=elepant_grass_genome.fa O=elepant_grass_genome.dict

INFO2023-12-16 13:02:26CreateSequenceDictionary

********** NOTE: Picard's command line syntax is changing.

**********

********** For more information, please see:

********** 

https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

**********

********** The command line looks like this in the new syntax:

**********

**********    CreateSequenceDictionary -R elepant_grass_genome.fa -O elepant_grass_genome.dict

**********

13:02:26.574 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 13:02:26 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 13:02:26 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: 19285 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: 21936 Killed                  bwa index $fa

gtf file not provide, try get gtf from gff:

RUN CMD: gffread  elepant_grass_genomenew.gff -T -o elepant_grass_genomenew.gtf

build ANNOVAR index

RUN CMD: gtfToGenePred -genePredExt elepant_grass_genomenew.gtf unknown_refGene.txt

elepant_grass_genomenew.gtf doesn't appear to be a GTF file (GFF not supported by this program)

RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile elepant_grass_genome.fa  unknown_refGene.txt --out unknown_refGeneMrna.fa

Error: cannot read from regionfile unknown_refGene.txt: No such file or directory

INFO:    Cleaning up image...