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cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
https://iguide.readthedocs.io/en/latest/
GNU General Public License v3.0
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Failure at iguide_evaluation: NAs in widths (99% complete) #78

Closed ShanSabri closed 3 years ago

ShanSabri commented 3 years ago

Hi Chris,

Thanks for this software -- I am having an issue processing a run through iGUIDE where the pipeline fails at the iGUIDE_evaluation at nearly 99% completion. I can't seem to figure out why exactly this errors out. I am processing with a 128Gb memory instance.

My colleague has successfully processed this exact data but with the R2leadMismatch : 15 specified in the config.yml whereas I have this set to R2leadMismatch : 3. I am calling the pipeline via iguide run IP095/configs/IP095.yml -- --notemp --nolock --cores 14 --restart-times 5.

Here's the last few lines of the snakelike log: 

[Fri Jan 22 21:48:53 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=8000

Trying to restart job 86.

[Fri Jan 22 21:49:02 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=16000

Trying to restart job 86.

[Fri Jan 22 21:49:10 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=24000

Trying to restart job 86.

[Fri Jan 22 21:49:19 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=32000

Trying to restart job 86.

[Fri Jan 22 21:49:28 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=40000

Trying to restart job 86.

[Fri Jan 22 21:49:37 2021]
rule iguide_evaluation:
    input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
    output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
    log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
    jobid: 86
    resources: mem_mb=48000

[Fri Jan 22 21:55:14 2021]
Finished job 659.
894 of 907 steps (99%) done
[Fri Jan 22 22:02:39 2021]
Finished job 658.
895 of 907 steps (99%) done
[Fri Jan 22 22:05:52 2021]
Finished job 661.
896 of 907 steps (99%) done
[Fri Jan 22 22:08:18 2021]
Finished job 660.
897 of 907 steps (99%) done
[Fri Jan 22 22:10:58 2021]
Finished job 662.
898 of 907 steps (99%) done
[Fri Jan 22 22:18:54 2021]
Finished job 664.
899 of 907 steps (99%) done
[Fri Jan 22 22:41:27 2021]
Finished job 663.
900 of 907 steps (99%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ubuntu/iGUIDE/.snakemake/log/2021-01-22T183409.805924.snakemake.log

/home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log:

iGUIDE Evaluation Inputs:
 Variables    Values
 config :     /home/ubuntu/iGUIDE/analysis/IP095/config.yml
 output :     /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds
 support :    /home/ubuntu/iGUIDE_runs/IP095/sampleInfo/supp.csv
 iguide_dir : /home/ubuntu/iGUIDE

Loading dependencies.
Importing experimental data and configurations.

Error in width(x) : NAs in 'x' are not supported
Calls: <Anonymous> ... .charToXStringSet -> solveUserSEW -> width -> width
Execution halted

Any help would be much appreciated. Thanks.

ShanSabri commented 3 years ago

Solved -- I was including an index for which no reads were demux'd to. After I remove that sample index then it runs without issue.