bed2annotation.pl fail

[Xiao Lei]

Dear Dr. Zhang,

I run bed2annotation.pl ( bieniaszs-ipro:hg19_NL4_3 bieniaszlab$ perl /usr/local/CTK/bed2annotation.pl -dbkey hg19 -ss -big -region -v -summary hnRNPU_hg19_tag.uniq.annot.summary.txt hnRNPU_hg19_tag.uniq.bed hnRNPU_hg19_tag.uniq.annot.txt ), this command runs around 15 minutes but it failed with message:

Use of uninitialized value $upstream_intergenicN_correct in subtraction (-) at /usr/local/CTK/bed2annotation.pl line 428.

Illegal division by zero at /usr/local/CTK/bed2annotation.pl line 434.

The summary files are:

Summary of region annotation

------------------------------

Region No. %

Total 6404037 100.0

Genic 0 0.0

Exon 0 0.0

CDS exon 0 0.0

5' UTR exon 0 0.0

3' UTR exon 0 0.0

Intron 0 0.0

Upstream 10K 0 0.0

Downstream 10K 0 0.0

Genic+ext10K        0 0.0

Deep intergeic 6404037 100.0

Percentage of intervals in each region (adjusted):

Region %

Any input would be much appreciated.

Xiao

[coy...@gmail.com]

Hi Xiao,

I have encountered the same error:

Use of uninitialized value $upstream_intergenicN_correct in subtraction (-) at /usr/bin/CTK/bed2annotation.pl line 428.
Illegal division by zero at /usr/bin/CTK/bed2annotation.pl line 434.

I also see 100% deep intergenic in the summary file:

Summary of region annotation
------------------------------

Region  No.     %

Total   4353801 100.0

Genic   0       0.0
Exon    0       0.0
CDS exon        0       0.0
5' UTR exon     0       0.0
3' UTR exon     0       0.0
Intron  0       0.0
Upstream 10K    0       0.0
Downstream 10K  0       0.0
Genic+ext10K    0       0.0

Deep intergeic  4353801 100.0

Percentage of intervals in each region (adjusted):
Region  %

Did you ever discover how to fix this issue?

Kind regards,

Steve

[Xiao Lei]

Hi, Steve,

Unfortunately, I never got any reply from this forum to solve my problem. After so much frustration, I switched to Paralyzer and wavCluste R to process my PAR-CLIP data, and they work. You can do the annotation following the instructions of wavCluste R, alternatively, if you have a cluster bed file, you can annotate with Homer.  

Best,

Xiao

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[Huijuan Feng]

Hi Xiao,

I am sorry we did not offer timely help on your issues.  But you are welcome to use CTK in the future and we will try our best to provide full support. Thanks!

Best,

Huijuan

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[Huijuan Feng]

Hi Steve,

We can help take a look at this issue if you could kindly provide the input file and command line you used for bed2annotation.pl. Thanks!

Best,

Huijuan

[coy...@gmail.com]

Hi Huijuan,

Thanks for the prompt reply.

Here is the command line that I've used:

perl /usr/bin/CTK/bed2annotation.pl -dbkey hg38 -ss -big -region -v -summary IGF2BP1_eclip_K562.tag.uniq.annot.summary.txt IGF2BP1_eclip_K562.tag.uniq.rgb.bed IGF2BP1_eclip_K562.tag.uniq.annot.txt 

Here is a dropbox link to the file: https://www.dropbox.com/s/p3g8fboh1we14b4/IGF2BP1_eclip_K562.tag.uniq.rgb.bed?dl=0

Thanks for any help you can provide. This is eCLIP data from the Yeo lab published in the Van Nostrand 2016 paper.

Steve

[xuan ye]

Hi,

How was this issue being solved?

I had the exact error with the top thread when annotating rgb.bed file using hg38 database.

Best,

Xuan

[Chaolin Zhang]

Hi Xuan,

One thing you can check is the name of the chromosomes - they should be chrN instead of N, to match the names in the annotation files.

Chaolin

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