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biomystery / atacCNV

A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data
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ERROR:root:Format "AUTO" cannot be recognized! of macs2 pileup #2

Open jiangye201315 opened 2 years ago

jiangye201315 commented 2 years ago

bedToBdgBw.sh was use macs pileup to generate pileup track (bw,bdg) from input reads (bed) with reads extend half of window size in both direction，such as : macs2 pileup -i $input -B --extsize $[window/2] -o ${bdg}. I have a PE sequence ATAC-seq data, and input the tagalign bed as the follow：

chr1 10045 10118 A00602:612:H3L2GDSX3:3:1661:14082:23531/1 30 + chr1 10045 10118 A00602:612:H3L2GDSX3:3:1661:14082:23531/2 30 - chr1 10057 10147 A00602:612:H3L2GDSX3:3:1141:2899:21010/1 12 + chr1 10057 10147 A00602:612:H3L2GDSX3:3:1141:2899:21010/2 12 - chr1 10069 10125 A00602:612:H3L2GDSX3:3:1630:24704:30436/2 30 + chr1 10069 10125 A00602:612:H3L2GDSX3:3:1630:24704:30436/1 30 - chr1 10087 10168 A00602:612:H3L2GDSX3:3:1241:21748:31516/2 12 + chr1 10087 10168 A00602:612:H3L2GDSX3:3:1241:21748:31516/1 12 - chr1 10147 10185 A00602:612:H3L2GDSX3:3:1414:4110:5666/2 30 + chr1 10147 10185 A00602:612:H3L2GDSX3:3:1414:4110:5666/1 30 -

I got a ERROR message: "ERROR:root:Format "AUTO" cannot be recognized!"

I don't know what`s wrong with this file, and how to deal with it?

princeps091-binf commented 1 year ago

I got the same error, but resolved it by specifying the file format (adding the argument "-f BED" to the command). Hope this helps!