Attempt to move input BAM file?

[tfenne]

Hi - I'm attempting to run parliament2 on an input BAM file and ran into some strange behaviour. At first I wasn't sure it was parliament2 ... I ran the tool and then noticed several hours later, mid-run, that the input BAM file outside the docker container had been truncated to 0 bytes long.

I was suspicious, but thought maybe I'd typo'd something and caused this. I re-generated the BAM file and then re-ran parliament2 but mounted the input volumes as read-only. When I did that I get the following message stating mv: cannot remove <path to input BAM inside container>. So it seems to me that p2 is trying to move the input, is that really the case? That seems like really bad behavior - there's nothing in the docs that says the inputs should be setup in a way that p2 is allowed to move/remove them at will!

[tfenne]

Looking in parliament2.sh I see the issue at line 123 in my case (and also at line 114). That also explains why my docker container for running p2 blows up to ~100GB very quickly. Could those copy statements not be replaced with symlinking so that a) the input files are removed/moved and b) the docker image doesn't blow up in size?

[MaestSi]

Hi,
I faced this issue too from version 0.1.9 on. The input bam file is moved to input.bam, and is not moved back when the jobs ends. I hope too this is going to be fixed in a future release.