bgzf_uncompress and bgzf_read errors with WGS bams

[tamuanand]

Are you using the latest version of samtools and [HTSlib]

yes
samtools 1.18

Please describe your environment.

• OS Linux 4.14.314-237.533.amzn2.x86_64
• machine architecture x86_64
• compiler gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0

I am running this using docker on AWS EC2 g4dn.12xlarge

• 4gpus, 48cpus, 192 GB RAM

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

I am trying to break down a huge bam file so that each file has 50M lines and then run bwakit on the split files as below

• 130GB fastq file broken down into 22 smaller files

Previously, I was getting some E::sam_parse1 errors as reported at #1932

Now I am getting these errors

[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error 1 after 21 of 40 bytes

Any ideas how to get around these?

Thanks in advance.

[jkbonfield]

Closing as this belongs in #1932 discussion.