Error in rule scoring

[WZo0o]

Hi,

When I run the workflow, I met the following error:

[Sun Jun 11 15:10:29 2023]
rule scoring:
    input: GRCh38.nr_deletions/matrix.bed, GRCh38.nr_deletions/matrix_100bpdown.bed, GRCh38.nr_deletions/matrix_100bpup.bed
    output: output/GRCh38.nr_deletions.score
    jobid: 2
    wildcards: set=GRCh38.nr_deletions

Submitted job 2 with external jobid '2915471.mu01'.
[Sun Jun 11 16:13:15 2023]
Error in rule scoring:
    jobid: 2
    output: output/GRCh38.nr_deletions.score
    conda-env: /data/wangzh/tools/CADD-SV/.snakemake/conda/9c6953c1
    shell:

        Rscript --vanilla scripts/scoring.R GRCh38.nr_deletions GRCh38.nr_deletions/matrix.bed GRCh38.nr_deletions/matrix_100bpdown.bed GRCh38.nr_deletions/matrix_100bpup.bed output/GRCh38.nr_deletions.score

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 2915471.mu01

Error executing rule scoring on cluster (jobid: 2, external: 2915471.mu01, jobscript: /data/wangzh/tools/CADD-SV/.snakemake/tmp.ffi1aqfz/snakejob.scoring.2.sh). For error details see the cluster log and the log files of the involved rule(s).

In order to solve the error, I run the shell command and met the following error:

Rscript --vanilla scripts/scoring.R GRCh38.nr_deletions GRCh38.nr_deletions/matrix.bed GRCh38.nr_deletions/matrix_100bpdown.bed GRCh38.nr_deletions/matrix_100bpup.bed output/GRCh38.nr_deletions.score
Error in Ops.data.frame(k[[2]], k[[5]]) :
  ‘+’ only defined for equally-sized data frames
Calls: caddsv -> Ops.data.frame
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Do you have any suggestions for me?

[makirc]

Hi, My best guess might be some additional characters/mis-formatting in your BED file. Would you be able to share it with me, so that I can have a look? (martin.kircher at bih-charite.de). Best, Martin

[WZo0o]

Hi, thanks for your help. I can my BED file with you and I am looking forward to your reply.

id_GRCh38.nr_deletions.zip

Best

[makirc]

Just a brief update. I could not see problems with the file, so I am currently running it through CADD-SV. My current hypothesis would be that a subjob was killed on your systems due to resource limitations (i.e. out of memory). Will keep you posted whether I can reproduce the error.

[WZo0o]

Thanks for your help and I am looking forward to your reply.

[makirc]

Just a brief update. It is still running (without any errors so far). I only gave it a very limited number of CPUs, not realizing that you had millions of SVs in your file. I will keep you posted about results. Generally would recommend to split up such big files in a number of parallel runs. Some annotations take considerably longer than others, limiting the parallelization by annotation which is implemented in our workflow.

[WZo0o]

Thanks for your nice notification and I am looking forward to your latest news.

[makirc]

Hi there, I can reproduce the problem. I think it is a single variant in the whole file. :(

chr4    0       705161  DEL

The coordinate range is correctly specified in BED format, but CADD-SV seems to need a coordinate that is at least 1, i.e.

chr4    1       705161  DEL

seems to work. I'll try to look into the code to fix that on our end, but it should be easy to have this workaround for now.

[WZo0o]

Thanks for your nice help