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mapleforest / HaploMerger2

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Got errors when I ran A3 and B1 #24

Open Haoran-Xue opened 5 years ago

Haoran-Xue commented 5 years ago

Dear Shengfeng,

I got expected results when I ran scripts A3 and B1 with the genome bbv18wm. However, I got the same error when I ran A3 and B1 with my own genome:

../bin/faDnaPolishing.pl --legalizing --noLeadingN --removeShortSeq=200

--legalizing=1 . --maskShortPortion=0 . --noLeadingN=1 . --removeShortSeq=200 . Problems with the fasta file; no symbol > found !

I'm sure that the entries in my genome file start with ">", like this: >1 TTGCACTGGTCTGACTGAATAGTTTCATTTCACCATGAATGACTTTGTGGAGcaacaaaa gaaatattttgCTGAACATGAacgtttttttttgttattccgAGCTGATTGTCCCGTTGA TATGCATGCTCTTGTTCAACTCATTTTCactgttattattattattataaaaaaactttt

Do you know why the > symbols in my file are not recognized?

Best regards, Haoran

mapleforest commented 5 years ago

Probably your fasta file is not in unix/linux TXT format. Try to convert them from DOS TXT to unix/linux TXT.

Haoran-Xue commented 5 years ago

Yeah, it worked after I converted them from DOS TXT to unix/linux TXT. Thank you so much!