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No CDS checked. #556

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oYZYo opened this issue Aug 19, 2024 · 1 comment
Open

No CDS checked. #556

oYZYo opened this issue Aug 19, 2024 · 1 comment

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@oYZYo
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oYZYo commented Aug 19, 2024

java -jar snpEff.jar build -gtf22 -v WBcel235

FATAL ERROR: No CDS checked. This is might be caused by differences in FASTA file transcript IDs respect to database's transcript's IDs.

Transcript IDs from database (sample):
'NR_067219.1'
'NR_066805.1'
'NR_067294.1'
'NM_001306396.3'
'NR_131382.1'
'NM_001380177.1'
'NM_001380175.2'
'NM_059160.7'
'NM_059158.7'
'NM_059159.4'
'NM_059157.8'
'NR_067277.1'
'NM_059156.7'
'NR_066628.1'
'NM_059155.9'
'NM_001128941.5'
'NM_059154.8'
'NR_066918.1'
'NR_066851.1'
'NR_066971.1'
'NR_067077.1'
'NR_067100.1'
Transcript IDs from database (fasta file):
'lcl|NC_003282.8_cds_NP_501649.2_16293'
'lcl|NC_003283.11_cds_NP_507118.1_24922'
'2_24447'
'8_8706'
'2_24443'
'8_8707'
'8_8708'
'2_24446'
'2_24441'
'lcl|NC_003283.11_cds_NP_001368552.1_18866'
'lcl|NC_003280.10_cds_NP_496939.2_9103'
'lcl|NC_003279.8_cds_CELE_Y71A12C.3_4080'
'lcl|NC_003281.10_cds_NP_001367874.1_10847'
'lcl|NC_003284.9_cds_NP_509080.2_27886'
'2_24437'
'lcl|NC_003283.11_cds_NP_001256941.1_26323'
'lcl|NC_003282.8_cds_NP_001255368.1_16208'
'2_24434'
'2_24435'
'lcl|NC_003284.9_cds_NP_509034.3_27816'
'lcl|NC_003282.8_cds_NP_500904.1_15057'
'121_18155'

@oYZYo
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oYZYo commented Aug 19, 2024

same issue occured when ran this:
./scripts/buildDbNcbi.sh WBcel235

@SusiJo SusiJo mentioned this issue Jan 23, 2025
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