BWA Suddenly says fail to open file

Question

[haiying.kong]

I am trying to rerun BWA on the same data with same code. It did not give any error message before, but this time, I got error message that says:

bwa mem $GATK_hg ../Data/${sample}_R1.fastq.gz ../Data/${sample}_R2.fastq.gz -t 4 > ${sample}.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs

[E::main_mem] fail to open file `../Data/T37370_R1.fastq.gz'.

It is with exactly same command on same data.

I am using the Version: 0.7.12-r1039

Answer 1

[dariober]

A couple of suggestions:

• Check gzipped fastq files are still intact, e.g. with gzip -t myfastq.gz

• Check your disk space is not full, e.g. df -h

Answer 2

[haiying.kong]

Ok. I figured out. I made symbolic link to the fastq data, and than I made change for the original data file directory.

Thank you so much for your help.