PacBio "recalladapters" on ec2 returning .tmp

Question

[aveadj]

I have a ec2 instance where I'm running Pacbio's "recalladapters" command. The output is being stored on an EBS volume.

recalladapters -j 10 --minSnr=2.0 --disableAdapterCorrection --subreadset "filename.subreadset.xml" -o "/mnt/outputs/filename.recalled"

The output of my recall adapters command are:

filename.recalled.bam2bam_1.log
filename.recalled.scraps.bam.tmp
filename.recalled.subreads.bam.tmp

Why am I getting .tmp files? I don't believe the program was killed. Am I missing something?

I could run it again, but it costs money for the GPU hours so I'd like to avoid trial and error.

[aveadj]

Is it possible my EBS isn't big enough to hold the output? I see the drive is 228/250 used, possibly just running out of space?

[aveadj]

Situation resolved itself... just waited and it output the correct files? bewilders me

Answer 1

[Billy Rowell]

recalladapters writes .tmp files that are renamed when the command finishes. The command was still running when you saw .tmp files.