Creating merged peak sets in output directory out_dir Error in bed$thickStart : $ operator is invalid for atomic vectors

[ChangshengWei97]

Hi, thank you for this script. However, I meet the following error when I run:

[rcorces]

Not enough information to help. Likely is a problem with your input to the script. If you would like additional help, provide a fully reproducible example.

[ChangshengWei97]

Not enough information to help. Likely is a problem with your input to the script. If you would like additional help, provide a fully reproducible example.

Thank you for your answer, here is my input code:

Rscript createIterativeOverlapPeakSet.R --metadata /path/to/rawdata/metadata.txt --macs2dir /path/to/rawdata/summit02/ --outdir /path/to/rawdata/out_dir/ --suffix _summits.bed --blacklist /path/to/rawdata/blacklist/mm10-blacklist.v2.bed --genome mm10 --spm 5 --rule "(n+1)/2" --extend 250

and I got this error:

Creating merged peak sets in output directory /path/to/rawdata/out_dir/
Error in bed$thickStart : $ operator is invalid for atomic vectors
Calls: import.bed ... import.bed -> import -> import -> import -> import -> .local
停止执行

[ChangshengWei97]

Not enough information to help. Likely is a problem with your input to the script. If you would like additional help, provide a fully reproducible example.

and here is my metadata

here are my *_summits files in summit02

[rcorces]

Thanks for providing that additional information.
It looks like your issue is related to the format of the summits files
Should look like this

[rcorces@pelayo peakCalls]$ head WTC11-1_sort_dedup_summits.bed 
chr1    191502  191503  WTC11-1_sort_dedup_peak_1       12.1751
chr1    268038  268039  WTC11-1_sort_dedup_peak_2       17.5137
chr1    586194  586195  WTC11-1_sort_dedup_peak_3       10.9101
chr1    778411  778412  WTC11-1_sort_dedup_peak_4a      12.1751
chr1    778642  778643  WTC11-1_sort_dedup_peak_4b      52.1981
chr1    778848  778849  WTC11-1_sort_dedup_peak_4c      57.4147
chr1    779168  779169  WTC11-1_sort_dedup_peak_4d      17.5137
chr1    827098  827099  WTC11-1_sort_dedup_peak_5       4.09816
chr1    827444  827445  WTC11-1_sort_dedup_peak_6       14.7919
chr1    844613  844614  WTC11-1_sort_dedup_peak_7       5.12197

Did you get these files from MACS2 output? They dont look like it.

[ChangshengWei97]

Thanks for providing that additional information. It looks like your issue is related to the format of the summits files Should look like this

[rcorces@pelayo peakCalls]$ head WTC11-1_sort_dedup_summits.bed 
chr1    191502  191503  WTC11-1_sort_dedup_peak_1       12.1751
chr1    268038  268039  WTC11-1_sort_dedup_peak_2       17.5137
chr1    586194  586195  WTC11-1_sort_dedup_peak_3       10.9101
chr1    778411  778412  WTC11-1_sort_dedup_peak_4a      12.1751
chr1    778642  778643  WTC11-1_sort_dedup_peak_4b      52.1981
chr1    778848  778849  WTC11-1_sort_dedup_peak_4c      57.4147
chr1    779168  779169  WTC11-1_sort_dedup_peak_4d      17.5137
chr1    827098  827099  WTC11-1_sort_dedup_peak_5       4.09816
chr1    827444  827445  WTC11-1_sort_dedup_peak_6       14.7919
chr1    844613  844614  WTC11-1_sort_dedup_peak_7       5.12197

Did you get these files from MACS2 output? They dont look like it.

Thank you for your answer. YES, I get _summits.bed files from MACS2,
here is my code
macs2 callpeak -t ctrl_1_final.bam --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01 -n ctrl_1

and this is my summits files: