BWA-MEM alignment error with hg38 from GATK

Question

[win]

hi all, i downloaded a bam file from 1000 genomes

HG00100.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam

then i converted this to fastq using

sudo java -jar algorithms/picard/picard.jar SamToFastq VALIDATION_STRINGENCY=SILENT I=data/HG100.bam FASTQ=data/HG100.1.fastq SECOND_END_FASTQ=data/HG100.2.fastq UNPAIRED_FASTQ=data/HG100.unpaired.fastq

I have hg38 fasta and all associated indices from

https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

next i would like to align my fastq to hg38, the command i use is as follows

sudo ./algorithms/bwa-align/bwa mem -M references/hg38.fasta data/HG100.1.fastq data/HG100.2.fastq  > data/HG100.aligned.reads.sam

PROBLEM: i am getting a segmentation fault error when i use the hg38 from GATK HG38 bundle. HOWEVER, the above works fine when I use the hg38 from UCSC.

any ideas why i am unable to use the GATK version?

thanks in advance.

[Pierre Lindenbaum]

sudo ....

please , don't

[win]

ok, wont. will change

[Santosh Anand]

what's the exact error message?

[win]

core dumped. segmentation fault.

[win]

turns out the reference fasta file was corrupt for some reason.

[h.mon]

Be aware it is recommended to shuffle the bam file previous to converting from bam to fastq.