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My fast file is not found by GenomeAnalysisTK

I was trying to run GATK but my fasta file can't be detected by the program. Though the fasta exists but it showing that the file is not exist.

My lines was:

java -Xmx16G -jar /Users/ZILLURRAHMAN/Desktop/PhD/GATK/GenomeAnalysisTK.jar -T PrintReads -R /Users/ZILLURRAHMAN/Desktop/PhD/Apicomplexan/Babesia_microti/Data/Strain_Naushon/strain_naushan.fasta -I /Users/ZILLURRAHMAN/Desktop/PhD/Apicomplexan/Babesia_microti/Data/Strain_Naushon/Naushon.sorted.bam -BQSR recalibration_report.grp -o strain_naushan_bqsr.bam

ERROR MESSAGE: Fasta dict file /Users/ZILLURRAHMAN/Desktop/PhD/Apicomplexan/Babesia_microti/Data/Strain_Naushon/strain_naushan.dict for reference /Users/ZILLURRAHMAN/Desktop/PhD/Apicomplexan/Babesia_microti/Data/Strain_Naushon/strain_naushan.fasta does not exist. Please see for help creating it.
ERROR ------------------------------------------------------------------------------------------

MacBook-Pro:GATK ZILLURRAHMAN$ cd /Users/ZILLURRAHMAN/Desktop/PhD/Apicomplexan/Babesia_microti/Data/Strain_Naushon/
MacBook-Pro:Strain_Naushon ZILLURRAHMAN$ ls
Naushon.sorted.bam SRR901625_1.fastq SRR901625_2.fastq strain_naushan.fasta.fai
Naushon.sorted.vcf SRR901625_1.fastq.gz SRR901625_2.fastq.gz strain_naushan.fasta wgs.fasta
MacBook-Pro:Strain_Naushon ZILLURRAHMAN$ ls -sh
total 36563568
2340032 Naushon.sorted.bam 3712872 SRR901625_1.fastq.gz 8 12672 wgs.fasta
1148896 Naushon.sorted.vcf 12817944 SRR901625_2.fastq 12672 strain_naushan.fasta
12817944 SRR901625_1.fastq 3700520 SRR901625_2.fastq.gz 8 strain_naushan.fasta.fai
MacBook-Pro:Strain_Naushon ZILLURRAHMAN$

Best Answer


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