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BWA and fastqtosam failing with read names do not match errors
I'm using the GATK best practices to call public exome data. Out of over 600 exomes, most of the samples did fine with BWA mem alignment and fastqtosam. About 100 samples failed both steps (the same samples failed both). For fastqtosam an empty file is created. For BWA a very small file is created. The input for both these steps is paired end FASTQ files from a public repository. The error messages from both processes mention read names not matching, for instance this is from fastqtosam:
Exception in thread "main" picard.PicardException: In paired mode, read name 1 (SRR221230.sra.ncbi_enc.1) does not match read name 2 (SRR221230.sra.ncbi_enc.4)
Can anyone tell me what is causing this and if there is a way to recover the data for these samples?