oushujun
commented
4 days ago Please check the SINE folder in the A D subgenome. It may be too large for AnnoSINE to handle.
Shujun
On Tue, Oct 8, 2024 at 11:30 PM Apl-cc @.***> wrote:
Hi Dr. Shujun,
EDTA is a very good software！ Recently, I also encountered a problem when annotating TE sequences in the IWGSCv1p1A.fa genome with EDTA. The error message is as follows: No SINE results were found! v2.2.0
Start to find SINE candidates.
cp: cannot stat 'IWGSCv1p1A.fa.mod.SINE.raw.fa': No such file or directory Error: SINE results not found!
ERROR: Raw SINE results not found in IWGSCv1p1A.fa.mod.EDTA.raw/IWGSCv1p1A.fa.mod.SINE.raw.fa If you believe the program is working properly, this may be caused by the lack of SINEs in your genome.
The IWGSC genome has three subgenomes (A, B, and D). When I annotated the B genome, it worked properly, but the A and D genomes encountered the above problems, In addition, I also successfully annotated a genome using EDTA. And these files were generated in the raw/SINE folder
1359834c85e311efadb2b4055db3aef5 55a8c0b0857e11ef9caab4055db3aef5 b8f5b0b6857811efa898b4055db3a915 d0ad680c801911efb3ddb4055db3a915 HMM_out IWGSCv1p1A.fa_0150c31885e311efadb2b4055db3aef5.mod IWGSCv1p1A.fa_190dd9887fcf11efb3ddb4055db3a915-matches.fasta IWGSCv1p1A.fa_190dd9887fcf11efb3ddb4055db3a915.mod IWGSCv1p1A.fa_456360a2857e11ef9caab4055db3aef5.mod IWGSCv1p1A.fa_a8b2e714857811efa898b4055db3a915.mod IWGSCv1p1A.fa.mod -> ../../IWGSCv1p1A.fa.mod Step1_extend_tsd_input_1.fa Step1_extend_tsd_input_2.fa Step1_extend_tsd_input.fa Step2_extend_blast_input.fa Step2_extend_blast_input_rename.fa Step2_tsd_output.fa Step2_tsd.txt Step3_blast_output.paf
Any good suggestions to solve this problem?
pengliang
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Apl-cc
Hi Dr. Shujun,
EDTA is a very good software！ Recently, I also encountered a problem when annotating TE sequences in the IWGSCv1p1A.fa genome with EDTA. The error message is as follows: No SINE results were found! v2.2.0
Start to find SINE candidates.
cp: cannot stat 'IWGSCv1p1A.fa.mod.SINE.raw.fa': No such file or directory Error: SINE results not found!
ERROR: Raw SINE results not found in IWGSCv1p1A.fa.mod.EDTA.raw/IWGSCv1p1A.fa.mod.SINE.raw.fa If you believe the program is working properly, this may be caused by the lack of SINEs in your genome.
The IWGSC genome has three subgenomes (A, B, and D). When I annotated the B genome, it worked properly, but the A and D genomes encountered the above problems, In addition, I also successfully annotated a genome using EDTA. And these files were generated in the raw/SINE folder
1359834c85e311efadb2b4055db3aef5 55a8c0b0857e11ef9caab4055db3aef5 b8f5b0b6857811efa898b4055db3a915 d0ad680c801911efb3ddb4055db3a915 HMM_out IWGSCv1p1A.fa_0150c31885e311efadb2b4055db3aef5.mod IWGSCv1p1A.fa_190dd9887fcf11efb3ddb4055db3a915-matches.fasta IWGSCv1p1A.fa_190dd9887fcf11efb3ddb4055db3a915.mod IWGSCv1p1A.fa_456360a2857e11ef9caab4055db3aef5.mod IWGSCv1p1A.fa_a8b2e714857811efa898b4055db3a915.mod IWGSCv1p1A.fa.mod -> ../../IWGSCv1p1A.fa.mod Step1_extend_tsd_input_1.fa Step1_extend_tsd_input_2.fa Step1_extend_tsd_input.fa Step2_extend_blast_input.fa Step2_extend_blast_input_rename.fa Step2_tsd_output.fa Step2_tsd.txt Step3_blast_output.paf
Any good suggestions to solve this problem?
pengliang