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Format error during training of closely related species #417

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zhanghongbin01 opened this issue Jul 7, 2024 · 0 comments
Open

Format error during training of closely related species #417

zhanghongbin01 opened this issue Jul 7, 2024 · 0 comments

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@zhanghongbin01
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When I run this command to train related species, the following error message will appear. Is this the reason for the format of the genome and gff files, and what format should be modified

command:
autoAugTrain.pl --genome=./Ncolo/ncol.fa --trainingset=./Ncolo/Ncol.gff3 --species=ncol

error:
1 - WARNING: Detected whitespace in fasta header of file /mnt/sda/zhb/workspace/03zhushi_final_alba/02_structure/01_denovo_prediction/Ncolo/ncol.fa. This may later on cause problems! If the pipeline turns out to crash, please clean up the fasta headers, e.g. by using simplifyFastaHeaders.pl. This message will be suppressed from now on!
1io was~inoadeveovefile /mnt/sda/zhb/workspace/03zhushi_final_alba/02_structure/01_denovo_prediction/Ncolo/ncol.fa. This may later on cause problems! If the pipeline turns out to crash, please clean up the fasta headers, e.g. by using simplifyFastaHeaders.pl. This message will be suppressed from now on!
1 - WARNING: Fasta headers in file /mnt/sda/zhb/workspace/03zhushi_final_alba/02_structure/01_denovo_prediction/Ncolo/ncol.fa seem to contain non-letter and non-number characters. That means they may contain some kind of special character. This may later on cause problems! If the pipeline turns out to crash, please clean up the fasta headers, e.g. by using simplifyFastaHeaders.pl. This message will be suppressed from now on!
Error: UTR interval in CDS range of gene Nycol.A01185.2.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A01335.10.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A02722.4.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A00240.12.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A03106.2.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A00512.4.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A01794.5.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A00282.6.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A01794.4.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.
Error: UTR interval in CDS range of gene Nycol.A03226.1.v1.2 on sequence GWHAAYW00000001. Ignoring UTR in this case.

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