names attribute must be the same length as the vector

[Robin-Rounthwaite]

I get quite far into the pipeline before crashing now. But I still crash during the running of an sveval step.

(on /private/groups/patenlab/rrounthw/sveval/snakemake in mustard)

I have no name!@9bf86e5c67f5:/app$ snakemake --configfile config.yaml --cores 4
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job          count    min threads    max threads
---------  -------  -------------  -------------
all              1              1              1
bgzip            2              1              1
parseeval        8              1              1
sveval           8              1              1
vcfnorm          2              1              1
total           21              1              1

Select jobs to execute...

[Tue Jun 27 22:21:04 2023]
rule bgzip:
    input: vcf/hsvlr-normalized-hg002.vcf
    output: vcf/hsvlr-normalized-hg002.vcf.gz
    jobid: 15
    reason: Missing output files: vcf/hsvlr-normalized-hg002.vcf.gz
    wildcards: vcf=vcf/hsvlr-normalized-hg002
    resources: tmpdir=/tmp


[Tue Jun 27 22:21:04 2023]
rule bgzip:
    input: vcf/hsvlr-unnormalized-hg002.vcf
    output: vcf/hsvlr-unnormalized-hg002.vcf.gz
    jobid: 4
    reason: Missing output files: vcf/hsvlr-unnormalized-hg002.vcf.gz
    wildcards: vcf=vcf/hsvlr-unnormalized-hg002
    resources: tmpdir=/tmp

[Tue Jun 27 22:21:15 2023]
Finished job 15.
1 of 21 steps (5%) done
Select jobs to execute...

[Tue Jun 27 22:21:15 2023]
rule vcfnorm:
    input: vcf/hsvlr-normalized-hg002.vcf.gz
    output: vcf/hsvlr-normalized-hg002.norm.vcf.gz
    jobid: 14
    reason: Missing output files: vcf/hsvlr-normalized-hg002.norm.vcf.gz; Input files updated by another job: vcf/hsvlr-normalized-hg002.vcf.gz
    wildcards: exp=hsvlr, method=normalized, sample=hg002
    resources: tmpdir=/tmp

[Tue Jun 27 22:21:15 2023]
Finished job 4.
2 of 21 steps (10%) done
Select jobs to execute...

[Tue Jun 27 22:21:15 2023]
rule vcfnorm:
    input: vcf/hsvlr-unnormalized-hg002.vcf.gz
    output: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz
    jobid: 3
    reason: Missing output files: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz; Input files updated by another job: vcf/hsvlr-unnormalized-hg002.vcf.gz
    wildcards: exp=hsvlr, method=unnormalized, sample=hg002
    resources: tmpdir=/tmp

Lines   total/split/realigned/skipped:  6532591/59167/556119/0
Lines   total/split/realigned/skipped:  6592250/0/0/0
Lines   total/split/realigned/skipped:  6547419/59200/558171/0
Lines   total/split/realigned/skipped:  6607107/0/0/0
[Tue Jun 27 22:21:44 2023]
Finished job 3.
3 of 21 steps (14%) done
Select jobs to execute...

[Tue Jun 27 22:21:44 2023]
rule sveval:
    input: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz
    output: rdata/sveval-hsvlr-unnormalized-hg002-all-call.RData
    jobid: 2
    reason: Missing output files: rdata/sveval-hsvlr-unnormalized-hg002-all-call.RData; Input files updated by another job: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz
    wildcards: exp=hsvlr, method=unnormalized, sample=hg002, region=all, eval=call
    resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630, runtime=30


[Tue Jun 27 22:21:44 2023]
rule sveval:
    input: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-call.RData
    jobid: 9
    reason: Missing output files: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-call.RData; Input files updated by another job: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz
    wildcards: exp=hsvlr, method=unnormalized, sample=hg002, region=nonrep, eval=call
    resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630, runtime=30


[Tue Jun 27 22:21:44 2023]
rule sveval:
    input: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-geno.RData
    jobid: 11
    reason: Missing output files: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-geno.RData; Input files updated by another job: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz
    wildcards: exp=hsvlr, method=unnormalized, sample=hg002, region=nonrep, eval=geno
    resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630, runtime=30

[Tue Jun 27 22:21:44 2023]
Finished job 14.
4 of 21 steps (19%) done
Select jobs to execute...

[Tue Jun 27 22:21:44 2023]
rule sveval:
    input: vcf/hsvlr-normalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-normalized-hg002-nonrep-geno.RData
    jobid: 21
    reason: Missing output files: rdata/sveval-hsvlr-normalized-hg002-nonrep-geno.RData; Input files updated by another job: vcf/hsvlr-normalized-hg002.norm.vcf.gz
    wildcards: exp=hsvlr, method=normalized, sample=hg002, region=nonrep, eval=geno
    resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630, runtime=30

Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [1]
Calls: svevalOl -> colnames<-
Execution halted
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [1]
Calls: svevalOl -> colnames<-
Execution halted
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [1]
Calls: svevalOl -> colnames<-
Execution halted
[Tue Jun 27 22:22:16 2023]
[Tue Jun 27 22:22:16 2023]
Error in rule sveval:
    jobid: 11
    input: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-geno.RData
    shell:
        Rscript sveval.R vcf/hsvlr-unnormalized-hg002.norm.vcf.gz vcf/hsvlr-truth-baseline.norm.vcf.gz hg002 False bed/hg38_non_repeats.bed geno rdata/sveval-hsvlr-unnormalized-hg002-nonrep-geno.RData 0.5
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Error in rule sveval:
    jobid: 21
    input: vcf/hsvlr-normalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-normalized-hg002-nonrep-geno.RData
    shell:
        Rscript sveval.R vcf/hsvlr-normalized-hg002.norm.vcf.gz vcf/hsvlr-truth-baseline.norm.vcf.gz hg002 False bed/hg38_non_repeats.bed geno rdata/sveval-hsvlr-normalized-hg002-nonrep-geno.RData 0.5
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Jun 27 22:22:16 2023]
Error in rule sveval:
    jobid: 9
    input: vcf/hsvlr-unnormalized-hg002.norm.vcf.gz, vcf/hsvlr-truth-baseline.norm.vcf.gz, bed/hg38_non_repeats.bed
    output: rdata/sveval-hsvlr-unnormalized-hg002-nonrep-call.RData
    shell:
        Rscript sveval.R vcf/hsvlr-unnormalized-hg002.norm.vcf.gz vcf/hsvlr-truth-baseline.norm.vcf.gz hg002 False bed/hg38_non_repeats.bed call rdata/sveval-hsvlr-unnormalized-hg002-nonrep-call.RData 0.5
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Jun 27 22:22:29 2023]
Finished job 2.
5 of 21 steps (24%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-06-27T222104.208617.snakemake.log