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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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Each of the 2 combined objects has sequence levels not in the other: #40

Closed storytc closed 3 years ago

storytc commented 3 years ago

Hi there, I'm really appreciate your brilliant tool for enrichment analysis. But when I try to create my own reference dataset, I got the warnings:

Warning messages:

1: In dir.create(cacheDir, recursive = TRUE) :
  'D:\APP\R-4.0.3\library\LOLA\mydata\danrer11\my_dataset' already exists
2: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrUn_KN149687v1, chrUn_KN149729v1, chrUn_KN149738v1, chrUn_KN149739v1, chrUn_KN149743v1, chrUn_KN149745v1, chrUn_KN149779v1, chrUn_KN149794v1, chrUn_KN149813v1, chrUn_KN149822v1, chrUn_KN149857v1, chrUn_KN149915v1, chrUn_KN149926v1, chrUn_KN149950v1, chrUn_KN149955v1, chrUn_KN149967v1, chrUn_KN149997v1, chrUn_KN150000v1, chrUn_KN150002v1, chrUn_KN150037v1, chrUn_KN150039v1, chrUn_KN150070v1, chrUn_KN150086v1, chrUn_KN150100v1, chrUn_KN150110v1, chrUn_KN150112v1, chrUn_KN150152v1, chrUn_KN150165v1, chrUn_KN150185v1, chrUn_KN150218v1, chrUn_KN150254v1, chrUn_KN150255v2, chrUn_KN150286v1, chrUn_KN150289v1, chrUn_KN150330v1, chrUn_KN150352v2, chrUn_KN150354v1, chrUn_KN150362v1, chrUn_KN150363v1, chrUn_KN150380v1, chrUn_KN150383v1, chrUn_KN150421v1, chrUn_KN150430v1, chrUn_KN150481v1, chrUn_KN150485v1, chrUn_KN150504v1, chrUn_KN150523v1, chrUn_KN150544v1, chrUn_KN150550v1, chrUn_KN150562v1, chrUn_KN150575v1, c [... truncated]
3: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrUn_KN149687v1, chrUn_KN149738v1, chrUn_KN149745v1, chrUn_KN149747v1, chrUn_KN149811v1, chrUn_KN149841v1, chrUn_KN149857v1, chrUn_KN149861v1, chrUn_KN149874v1, chrUn_KN149915v1, chrUn_KN149916v1, chrUn_KN149926v1, chrUn_KN149950v1, chrUn_KN150008v1, chrUn_KN150037v1, chrUn_KN150039v1, chrUn_KN150065v1, chrUn_KN150086v1, chrUn_KN150100v1, chrUn_KN150136v1, chrUn_KN150141v1, chrUn_KN150152v1, chrUn_KN150213v1, chrUn_KN150218v1, chrUn_KN150228v1, chrUn_KN150324v1, chrUn_KN150352v2, chrUn_KN150354v1, chrUn_KN150380v1, chrUn_KN150411v1, chrUn_KN150421v1, chrUn_KN150430v1, chrUn_KN150439v1, chrUn_KN150481v1, chrUn_KN150485v1, chrUn_KN150504v1, chrUn_KN150544v1, chrUn_KN150623v1, chrUn_KZ115963v1, chrUn_KZ115976v1, chrUn_KZ115993v1, chrUn_KZ116046v1, chrUn_KZ116047v1, chrUn_KZ116053v1, chrUn_KN148869v2, chrUn_KN149722v1, chrUn_KN149730v1, chrUn_KN149755v1, chrUn_KN149762v1, chrUn_KN149765v1, chrUn_KN149768v1, c [... truncated]
4: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrUn_KN149687v1, chrUn_KN149729v1, chrUn_KN149741v1, chrUn_KN149745v1, chrUn_KN149747v1, chrUn_KN149760v1, chrUn_KN149803v1, chrUn_KN149810v1, chrUn_KN149811v1, chrUn_KN149841v1, chrUn_KN149855v1, chrUn_KN149857v1, chrUn_KN149861v1, chrUn_KN149874v1, chrUn_KN149915v1, chrUn_KN149916v1, chrUn_KN149926v1, chrUn_KN149950v1, chrUn_KN149997v1, chrUn_KN150008v1, chrUn_KN150037v1, chrUn_KN150039v1, chrUn_KN150065v1, chrUn_KN150079v1, chrUn_KN150086v1, chrUn_KN150112v1, chrUn_KN150185v1, chrUn_KN150213v1, chrUn_KN150228v1, chrUn_KN150342v1, chrUn_KN150351v1, chrUn_KN150352v2, chrUn_KN150354v1, chrUn_KN150366v1, chrUn_KN150375v1, chrUn_KN150399v1, chrUn_KN150411v1, chrUn_KN150481v1, chrUn_KN150485v1, chrUn_KN150504v1, chrUn_KN150544v1, chrUn_KN150575v1, chrUn_KN150602v1, chrUn_KN150614v1, chrUn_KN150623v1, chrUn_KN150647v1, chrUn_KZ115963v1, chrUn_KZ115982v1, chrUn_KZ116008v1, chrUn_KZ116024v1, chrUn_KZ116046v1, c [... truncated]
5: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrUn_KN147632v2, chrUn_KN147636v1, chrUn_KN147652v2, chrUn_KN149683v1, chrUn_KN149685v1, chrUn_KN149687v1, chrUn_KN149688v2, chrUn_KN149689v2, chrUn_KN149691v1, chrUn_KN149694v1, chrUn_KN149698v1, chrUn_KN149702v1, chrUn_KN149705v1, chrUn_KN149716v1, chrUn_KN149717v1, chrUn_KN149719v1, chrUn_KN149723v1, chrUn_KN149725v1, chrUn_KN149741v1, chrUn_KN149743v1, chrUn_KN149745v1, chrUn_KN149747v1, chrUn_KN149749v1, chrUn_KN149760v1, chrUn_KN149778v1, chrUn_KN149794v1, chrUn_KN149795v1, chrUn_KN149803v1, chrUn_KN149805v1, chrUn_KN149810v1, chrUn_KN149811v1, chrUn_KN149812v1, chrUn_KN149813v1, chrUn_KN149841v1, chrUn_KN149852v1, chrUn_KN149856v1, chrUn_KN149861v1, chrUn_KN149884v1, chrUn_KN149893v1, chrUn_KN149904v1, chrUn_KN149912v1, chrUn_KN149915v1, chrUn_KN149939v1, chrUn_KN149946v1, chrUn_KN149949v1, chrUn_KN149950v1, chrUn_KN149967v1, chrUn_KN149968v1, chrUn_KN149973v1, chrUn_KN149998v1, chrUn_KN150000v1, c [... truncated]

I have eight reference datasets under the regions/ directory, all download from UCSC in bed format. It seems like these bed files doesn't have the same chrmosome numbers? But the eight files should be in different. I have no idea for these warnings. Thank you so much for your answer!

Best Ariel

nsheff commented 3 years ago

Did you close the issue because you were able to solve the problem?

storytc commented 3 years ago

I‘m not sure but feel sorry to bother you.... Any advice would be great...

nsheff commented 3 years ago

you just have to make sure you're using the same reference genome. if you have some of these random chromosomes in one file and not the other, you will get these warnings. it should still work.

storytc commented 3 years ago

yes, I think so. Thank you so much and sorry to bother you.