sambamba-markdup: unable to move file pointer

Question

[marongiu.luigi]

Dear all,

I have launched sambamba with this command:

sambamba markdup -r -t 8 --overflow-list-size 1000000 --hash-table-size \
1000000 <sorted.bam> <sortedFiltered.bam>

on two series of files. These are sorted bam files whose starting fastq are the same but are aligned to two different reference files.

On one set, the process is going through, but the other gave me the error: sambamba-markdup: unable to move file pointer.

What could be this error and how can I solve it?

Thank you

Answer 1

[marongiu.luigi]

Nothing, there was a space too much -- it was a typo. Case closed. This post can even be removed.

[ATpoint]

We'll leave it in case someone ever stumbles over the same issue. Anyway, thanks for following up, others may benefit from it in the future.