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BWA Suddenly says fail to open file

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

software error
• 9,694 views • link
written by haiying.kong haiying.kong

2 answers

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

• 1 views • link
written by dariober dariober

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.

• 1 views • link
written by haiying.kong haiying.kong

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