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I'm trying to run graph_peak_caller on a ATAC-seq data which is aligned to a single test chromosome graph which was generated with the PGGB pipeline. After aligning the raw data to the graph using vg map, when I try to run graph_peak_caller callpeaks -g ch19.nobg -s alignments.json, I see the following:
Hi,
I'm trying to run graph_peak_caller on a ATAC-seq data which is aligned to a single test chromosome graph which was generated with the PGGB pipeline. After aligning the raw data to the graph using
vg map
, when I try to rungraph_peak_caller callpeaks -g ch19.nobg -s alignments.json
, I see the following:Please let me know if any additional information would be helpful to determine what is going wrong.
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