Failure executing gater_unfltr_vcf in ManyWAGS

[gwigley409]

Hello, When running the ManyWAGS pipeline, I am running into a problem at the gather_unfltr_vcf step. It appears that the output.vcf.gz files are being generated, but the unfltr_vcf/all_vars.vcf.gz file is not. There is no log file in the .logs/gather_unfltr_vcf directory. The last few lines of the many_wags.err file are below.

[Sat Feb 24 09:54:21 2024] Finished job 354. 392 of 455 steps (86%) done Select jobs to execute...

[Sat Feb 24 09:54:23 2024] rule gather_unfltr_vcf: input: RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0000/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0001/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0002/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0003/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0004/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0005/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0006/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0007/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0008/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0009/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0010/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0011/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0012/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0013/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0014/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0015/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0016/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0017/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0018/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0019/output.vcf.gz, RESULTS/wgs/pipeline/UU_Cfam_GSD_1.0_ROSY/20240223/genotype_gvcfs/wags_0020/output.vcf.gz, 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mem_mb=200000, mem_mib=190735, disk_mb=1457, disk_mib=1390, tmpdir=, time=5760

Submitted job 10 with external jobid '14790504'. slurmstepd: error: JOB 14773457 ON a220 CANCELLED AT 2024-02-26T10:25:00 DUE TO TIME LIMIT

I would appreciate any help with this issue! It is very possible that I did something incorrectly.

[jonahcullen]

Hey there! Would you mind including the complete command you used for prep_joint.py? (I'm guessing it a "me" problem, nothing you did!)

[gwigley409]

source ~/.bashrc conda activate snakemake

python /scratch/negishi/gwigley/wags/wags/prep_joint.py \ --config /scratch/negishi/gwigley/WAGS_TEST/dog/UU_Cfam_GSD_1.0_ROSY_config.yaml \ --gvcfs /scratch/negishi/gwigley/WAGS_TEST/Many_WAGS_input.txt \ --snake-env snakemake \ --partition a \ --email gwigley@purdue.edu \ --account kje0003 \ --remote local \ --sif /scratch/negishi/gwigley/wags.sif \ --out /scratch/negishi/gwigley/WAGS_TEST/ManyWAGS

[jonahcullen]

Before doing more here, can you confirm that there are no other parts of the pipeline running? After that, if you could do a dry run, save the output like

snakemake -s many_wags.smk --configfile UU_Cfam_GSD_1.0_ROSY_config.yaml -np > DRY

and then attach the file here? I want to make sure I know where it left off in order to figure out where the issue cropped up.

[gwigley409]

DRY.txt

No other part of the pipeline was running. The output from the dry run is attached above

[jonahcullen]

And there was no gather_unfltr_vcf directory within .logs? If that is the case, have you tried restarting with sbatch?

[gwigley409]

The gather_unfltr_vcf directory is there, but there is nothing in it. I have tried restarting with sbatch and ran into the same problem

[jonahcullen]

Can you attach the err file from the latest attempt?

[gwigley409]

14773457.Many_WAGS_input_UU_Cfam_GSD_1.0_ROSY.many_wags.err.txt

The err file is attached above

[jonahcullen]

This is the one from last week no? I think you might have just hit the wall time before gather_unfltr_vcf could start. Could you try restarting it?

[gwigley409]

I tried to rerun the pipeline over the weekend and am still having the same issue. I have attached the err file. It seems like snakejob.gather_unfltr_vcf.10.sh is being submitted, but won't start running. It is just sitting in the queue until it times out. I have all the resources needed, so I'm not sure what is going on.

14872957.Many_WAGS_input_UU_Cfam_GSD_1.0_ROSY.many_wags.err.txt

[jonahcullen]

I'm a little confused as it looks like the whole pipeline restarted here? Did you potentially rename anything or make changes to any of the input? If gather_unfltr_vcf was submitted, there should be a directory with the same name in .logs. From that working directory, can you run find .logs -name "14886300*" and attach the err file? At the same, can you please do another dry run to confirm a restart would pick up from where it left off.

[gwigley409]

I figured out what the issue was, and its on my end. The snakejob.gather_unfltr_vcf.10.sh script is requesting Mem reserved: 200000M and we only have 128000M available to use for more than 24 hours. Is this the minimum value of memory needed? Or could I change it to a smaller amount? I appreciate your help!

[jonahcullen]

That's great and definitely you can turn this down. Perhaps try mem_mb = 100000?

[gwigley409]

I was able to run the pipeline successfully with mem_mb = 100000. Thank you for all of your help!

[jonahcullen]

Super!