Question

ChipQC 'names' attribute [9] must be the same length as the vector [2]'

1

Entering edit mode

ZheFrench ▴ 60

@zhefrench-11689

Last seen 12 weeks ago

France

I have a strange error when I call ChIPQC.

'names' attribute [9] must be the same length as the vector [2]

Number in brackets vary depending on the number of samples.

RNFC81 MCF10 POL2 unT7 unTreated 1 macs
RNFC84 MCF10 POL2 unT7 unTreated 2 macs
RNFC82 MCF10 POL2 T1 Tamoxifen 1 macs
RNFC85 MCF10 POL2 T1 Tamoxifen 2 macs
RNFC83 MCF10 POL2 T7 Tamoxifen 1 macs
RNFC86 MCF10 POL2 T7 Tamoxifen 2 macs
Compiling annotation...
Adding controls...
Computing metrics for 9 samples...
list
Bam file has 194 contigs
Error in names(res) <- nms :
  'names' attribute [9] must be the same length as the vector [2]
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply
In addition: Warning message:
stop worker failed:
  attempt to select less than one element in OneIndex

This is coming from this call.

experiment = ChIPQC(samples,annotation="hg38",chromosomes=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"),blacklist="hg38.blacklist.bed.gz")

Any help would be appreciated.

chipqc • 2.1k views

ADD COMMENT • link updated 6 months ago by bandconductor • 0 • written 4.1 years ago by ZheFrench ▴ 60

0

Entering edit mode

Hello,

I have a couple thoughts about this, but more information would be helpful. First- could you show what samples looks like? I assume you're trying to pass samples to the experiment argument to ChIPQC (and not the samples argument, in which case you'd want to refer to it specifically, and also provide the experiment argument in addition):

experiment = ChIPQC(some_experiment,   
    samples=samples,
    annotation="hg38",
    chromosomes=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"),
    blacklist="hg38.blacklist.bed.gz")

Another thought is that I notice ChIPQC uses BiocParallel::bplapply internally: I've had strange errors come from BiocParallel when simply not providing enough memory to R. I don't expect memory to be the issue, but I think it's always worth ruling out (if you are using a computing cluster and can easily just request more memory).

Best,

-Nick

P.S. I'm currently learning to help others.

ADD REPLY • link 4.0 years ago nick.eagles ▴ 100

score 1 · Answer 1 · 2021-01-22

1

Entering edit mode

Ishbel ▴ 10

@9053ac5d

Last seen 3.8 years ago

Hello,

I also encountered this problem these days. Then I found it caused by the absence of .bai files. You can generate .bai files by

samtools index file.bam

Best,

ADD COMMENT • link 3.8 years ago Ishbel ▴ 10

0

Entering edit mode

thanks! you have saved me so much time

ADD REPLY • link 6 months ago bandconductor • 0