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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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R step 12 "no"? #98

Closed YingChen94 closed 6 months ago

YingChen94 commented 7 months ago

It seems that Earl Grey has been running on step 12 "no" for a very long time. Is it normal? What is it working on?

 [1] "/usr/local/lib/R/bin/exec/R"
 [2] "--no-echo"
 [3] "--no-restore"
 [4] "--file=/usr/local/share/earlgrey-4.1.1-0/scripts//mergeRepeats.R"
 [5] "--args"
 [6] "/JT22M_EarlGrey/JT22M_mergedRepeats/looseMerge/JT22M.rmerge.gff.filtered"
 [7] "/JT22M_EarlGrey/JT22M_mergedRepeats/looseMerge/JT22M.mergedRepeats.bed"
 [8] "3994399550"
 [9] "/JT22M_EarlGrey/JT22M_mergedRepeats/looseMerge/JT22M.mergedRepeats.revisedTable"
[10] "/JT22M_EarlGrey/JT22M_mergedRepeats/looseMerge/JT22M.filteredRepeats.bed"
[11] "/JT22M_EarlGrey/JT22M_mergedRepeats/looseMerge/JT22M.filteredRepeats.summary"
[12] "no"
TobyBaril commented 6 months ago

This step is parsing your repeats to resolve overlaps and improve final annotations (the log posted is the output to show an Rscript is running), this can take a long time if you have a lot of repeats / very large files