deepbinner realtime does not quit after sleep 5
Opened this issue · 3 comments
Hi,
I hope this has an obvious answer.
I cannot figure out how to get deepbinner to exit its "waiting for new files" mode to continue a bash script/job that I submit to a HPC.
I transfer fast5 files in bulk (not real time) to a HPC and want to run deepbinner -> albacore -> porechop (trim only).
So for fast5 / non basecalled reads deepbinner realtime
is the correct approach, right?
Following @rrwick examples (thank you so much for your generosity) i do
where the variables
fast5dirs
is an array of foldernames and
NPROCS
is number of processes
mkdir demultiplexed_fast5s
for fast5 in ${fast5dirs[*]}; do
deepbinner realtime --omp_num_threads $NPROCS --in_dir $fast5 --out_dir demultiplexed_fast5s $librarytype
done
and from here let albacore cycle though the barcodeXX folders in the demultiplexed_fast5s folder.
In @rrwick s examples a Ctrl+C is needed from the user to end the deepbinner realtime program. But I cannot figure out how to get this into my bash script.
It might be something with the commands
trap break INT (https://www.unix.com/shell-programming-and-scripting/147781-doing-tail-script-then-return-back-continue-script.html)
and then perhaps sending a SIGINT ? However I am not at a skill level to get this to work.
Has anyone else got a solution working?
Edits: correct display of code block.
Hi,
i'm having a very similar problem caused by the need to manually interrupt the program. For the time being, i use a crude alteration in deepbinners realtime.py script.
I changed this section
else:
print('\nWaiting for new fast5 files (Ctrl-C to stop)', end='',
flush=True)
waiting = True
time.sleep(5)
to look like this:
else:
print('\nAll fast5 files processed, exiting')
quit()
time.sleep(5)
This lets me use deepbinner as part of a CWL-Workflow. Note that doing this will make the script useless for the intended "realtime" application where seqencing is still taking place during the execution of deepbinner. Hope it helps!
Hi,
I am having the same problem. I transfer my data to a server where I am running deepbinner through a jobscript. I am using deepbinner realtime
as my files are not basecalled. However I am stuck on "waiting for new files" and cannot get deepbinner to exit without deleting the job.
Is there a simple way around this without altering the realtime.py
script?
At the moment I am thinking about basecalling first and then running deepbinner classify and bin
.
Thank you @ttubb - your fix worked for me when I was having a similar issue.