The pipeline stalled at "chip.read_genome_tsv" for local backend

[erhei01]

Hi, team! I am trying the chip-seq-pipeline2 and atac-seq-pipeline using "local" backend. Both the pipeline stalled at "task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode".

About 5~6 days ago, The atac pipeline worked fine if I used "-i input.json" OR "-i https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json".But it distalled when I used '-i "./input.json" '. And now it always stalled at "task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode".

backend configure

backend=local

local-loc-dir=/disk/user_03/encode/tmp cromwell=/disk/user_03/.caper/cromwell_jar/cromwell-82.jar womtool=/disk/user_03/.caper/womtool_jar/womtool-82.jar

command line (at bash prompt)

conda activate encode caper run /disk/user_03/scripts/atac-seq-pipeline/atac.wdl -i input.json --singularity --max-concurrent-tasks 20

OS

x86_64 GNU/Linux

java -version

openjdk version "11.0.13" 2021-10-19 OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21) OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)

Any suggestions will be appreciated! Thank you very much!

cromwell.out.txt

[leepc12]

Sorry about late response.

Please check if singularity works on your system

$ singularity exec docker://ubuntu:latest echo hello
INFO:    Using cached SIF image
hello

Also please try with docker if you have docker installed on your system

$ docker run ubuntu:latest echo hello
hello

$ caper run /disk/user_03/scripts/atac-seq-pipeline/atac.wdl -i input.json --docker

[erhei01]

Hi, leepc12! Thanks for your help. Yes, the singularity did not return properly after "echo" ,so did it in the pipeline. I ran the pipeline in another station, it worked well. Indeed the singularity worked well at first and the pipeline worked well too. Thank you very much!