An error occurs when running the process with test data

tyewaichung commented 2 years ago

Hello When I used the encode chip-seq pipeline test data set to run the process today, the following error occurred and I don't know how to solve it.

Started troubleshooting workflow: id=8414c8ac-ac89-4579-95d0-9c6ae64b2fcb, status=Failed
Found failures JSON object. [ { "message": "Workflow failed", "causedBy": [ { "message": "Job chip.xcor:1:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.", "causedBy": [] }, { "message": "Job chip.xcor:0:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.", "causedBy": [] } ] **} ]
Recursively finding failures in calls (tasks)...

==== NAME=chip.xcor, STATUS=RetryableFailure, PARENT= SHARD_IDX=0, RC=1, JOB_ID=1142 START=2021-12-09T13:05:43.498Z, END=2021-12-09T13:05:52.396Z STDOUT=/home/zhong/chip-seq-pipeline2-2.1.2/chip/8414c8ac-ac89-4579-95d0-9c6ae64b2fcb/call-xcor/shard-0/execution/stdout STDERR=/home/zhong/chip-seq-pipeline2-2.1.2/chip/8414c8ac-ac89-4579-95d0-9c6ae64b2fcb/call-xcor/shard-0/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/zhong/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/zhong/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/zhong/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/zhong/miniconda**

How can I solve this kind of problem? Is it to delete the original conda environment and reinstall it? But after trying it, I found that it did not solve the problem

leepc12 commented 2 years ago

Did you try with the latest pipeline + caper (both released on 12/8/2021)?

tyewaichung commented 2 years ago

Did you try with the latest pipeline + caper (both released on 12/8/2021)?

Yes, I use the latest version of pipline and caper, but I found a problem. It may be that I did not re-init my backend, which caused the software used in the updated version environment to not be updated in time. I will try again now. I don't know if there will be any errors.

tyewaichung commented 2 years ago

Through the above attempts, the process has been successfully passed. If there are follow-up bugs that need to be resolved, I am asking you questions Thank you

ENCODE-DCC / chip-seq-pipeline2

An error occurs when running the process with test data #253