Hello, all!
Once again, apologies if I don’t do this correctly as I am new to the forum and nextflow.
I had an nf-core pipeline running last night, but it was killed due to memory purposes as I forgot to point to my custom config file.
Command:
nextflow run nf-core/ampliseq -params-file ./params.yaml -profile docker --metadata ./Metadata-fixed.txt --outdir ./results --save_intermediates --trunclenf 268 --trunclenr 268
I tried to -resume the run today by adding -resume marvelous_ardinghelli (previous run name) to my script.
Command:
nextflow run nf-core/ampliseq -params-file ./params.yaml -profile docker --metadata ./Metadata-fixed.txt --outdir ./results --save_intermediates --email megan.justice@okstate.edu --trunclenf 268 --trunclenr 268 -c nf.config -resume marvelous_ardinghelli
I got the following warning:
WARN: nf-core pipelines do not accept positional arguments. The positional argument
marvelous_ardinghelli
has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g.-profile test, docker
.
Thinking it did not correctly interpret my -resume command, and fearing it would just kick off a new instance of the pipeline, I hit enter and this resulted in the job Stopping:
[2]+ Stopped bash nextflow-ampliseq.sh.
Since then, I have been trying to resume my initial job (marvelous_ardinghelli) by changing the -resume from the run name to the session ID, but keep getting the notice that it is:
ERROR ~ Unable to acquire lock on session with ID 3a2485f9-35c8-4380-9288-2f7a15d1c93b
Common reasons for this error are:
- You are trying to resume the execution of an already running pipeline
- A previous execution was abruptly interrupted, leaving the session open
If I run lsof on the LOCK object, I see:
java 1657060 ec2-user 12uW REG 202,1 0 134568842 /home/ec2-user/Alexis16s/.next
[3] Exit 1 bash ./nextflow-ampliseq.sh
I found some documentation here https://nf-co.re/docs/usage/troubleshooting/aquire_lock_error
that says to remove the work directory. That makes me incredibly nervous, though.
So, instead I moved the work directory out of the folder I was working in, just one level higher, and am trying the same nextflow run command. However, I get the same issue of
Unable to acquire lock on session with ID
I have tried to clean up my directory by doing nextflow log, then nextflow clean . However, I get the same 'Unable to acquire lock on session with ID....'
issue.
Is there any way to recover the >24 hours of work that has already been done in my original nextflow run? I just need to resume it with my config file.