To execute picard run: java -jar $EBROOTPICARD/picard.jar

Question

[Azhar Jameel]

while finding depth by samtools facing the problem, please help to resolve it.

check depth

samtools flagstat \$bam_final/"$prefix".combo.bam > \$bam_final/"$prefix".combo.flagstat.txt
samtools depth \$bam_final/"$prefix".combo.bam | awk '{sum+=\$3} END {print "Average = ",sum/NR}' > \$bam_final/"$prefix".combo.depth.txt

error

To execute picard run: java -jar $EBROOTPICARD/picard.jar
awk: cmd. line:1: {sum+=$3} END {print Average = ,sum/NR}
awk: cmd. line:1:                                ^ syntax error

[Pierre Lindenbaum]

this is an awk error, it's unrelated to your title and unrelated to picard, but your $ are all escaped, so you're not running in a bash environment. You don't tell us all the informations. Otherwise, the awk command awk '{sum+=$3} END {print "Average = ",sum/NR}' is correct.

[Azhar Jameel]

align reads with bwa

bwa mem -M -t 8 \$ref \$trim/"$prefix"_forward_val_1.fq.gz \$trim/"$prefix"_reverse_val_2.fq.gz > \$sam/"$prefix".sam 2> \$log/"$prefix".bwape.log bwa mem -M \$ref \$trim/"$prefix"_forward_unpaired_1.fq.gz > \$sam/"$prefix"_1_unpaired.sam 2> \$log/"$prefix".bwase1.log bwa mem -M \$ref \$trim/"$prefix"_reverse_unpaired_2.fq.gz > \$sam/"$prefix"_2_unpaired.sam 2> \$log/"$prefix".bwase2.log

error is [E::bwa_idx_load_from_disk] fail to locate the index files

bwa index already run