ATAC-Seq MACS2 callpeak error

1

Hi, I’m trying to go through the ATAC-Seq Galaxy tutorial and I’m on the MACS2 callpeak step. It’s erroring out and I’m not sure what I got wrong. Here’s my history: Galaxy, and the Galaxy tutorial page: Hands-on: ATAC-Seq data analysis / ATAC-Seq data analysis / Epigenetics

Here’s the job run details:
{
“history_id”: “a28aaeab526eee15”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0”,
“tool_version”: “2.2.9.1+galaxy0”,
“inputs”: {
“treatment|t_multi_select”: “No”,
“treatment|input_treatment_file”: {
“batch”: false,
“product”: false,
“values”: [
{
“id”: “f9cad7b01a472135ac1b08019d9cc993”,
“src”: “hda”,
“map_over_type”: null
}
]
},
“control|c_select”: “No”,
“format”: “BED”,
“effective_genome_size_options|effective_genome_size_options_selector”: “2700000000”,
“nomodel_type|nomodel_type_selector”: “nomodel”,
“nomodel_type|extsize”: “200”,
“nomodel_type|shift”: “-100”,
“cutoff_options|cutoff_options_selector”: “qvalue”,
“cutoff_options|qvalue”: “0.05”,
“outputs”: [
“peaks_tabular”,
“summits”,
“bdg”
],
“advanced_options|to_large”: false,
“advanced_options|nolambda”: false,
“advanced_options|spmr”: false,
“advanced_options|ratio”: “”,
“advanced_options|slocal”: “”,
“advanced_options|llocal”: “”,
“advanced_options|broad_options|broad_options_selector”: “nobroad”,
“advanced_options|broad_options|call_summits”: true,
“advanced_options|keep_dup_options|keep_dup_options_selector”: “all”,
“advanced_options|d_min”: “20”,
“advanced_options|buffer_size”: “100000”
}
}

Thanks in advance!
Edwin

1 Like
2

Welcome, @Edwin_Huang1

Thanks for sharing all the details, it helped to take a look really quickly on our side!

Check the job run by clicking on the i-icon for one of your red error datasets. On that view, then click on the input BAM dataset to expand it. It is empty – so this tool had nothing to process and quit out.

Sometimes there will be another message in the job logs on that same view (further down) but your error is pretty technical. No input found, tool quit out.

Double check your steps from the start to confirm that the MarkDuplicates step is the only one that needs to be redone. Everything else looked fine to me from a quick scroll.

Hope this helps! :slight_smile: