我尝试在本地数据库上使用 psi-blast 并不断收到错误。 我认为我收到的错误可能是由于未正确创建blast数据库而导致的,因为当我使用命令创建数据库时:
makeblastdb -in smallmodified_scop_fa_represeq_lib_latest.fa -dbtype prot -out SCOPFAMBLAST_local_db
我得到以下输出:
Building a new DB, current time: 07/29/2024 19:24:58
New DB name: C:\Users\realt\OneDrive\Documents\Biology Projects\BioInfoDATABASES\SCOPFABLASTDF\SCOPFAMBLAST_local_db
New DB title: smallmodified_scop_fa_represeq_lib_latest.fa
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 154 sequences in 0.0448847 seconds.
BLAST Database error: Database memory map file error
我尝试忽略该错误并在数据库上运行 psi-blast 脚本,但我不断收到错误。 因此,我想首先解决这个问题,验证我的数据库是否良好,然后继续运行 psi-blast 脚本。
使用以下输入作为 fasta 文件,上面的命令应该会重现该问题:
>8072807_Q7UJS6_4003632
NERILLVDDDYSLLNTLKRNLSFDFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQYDLVTSKEELLKKT
>8072797_O51615_4003632
SKPRGINYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLDITMPKMDGITCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSVFVK
>8022848_2OP5_A_4001912
TDETAFLNSLFMDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNKEQHRISMVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIRS
>8107333_Q9HB45_4007725
FSTVKIIYTVGHSISIVALFVAITILVALRRLHCPRNYVHTQLFTTFILKAGAVFLKDAALFHSDDTDHCSFSTVLCKVSVAASHFATMTNFSWLLAEAVYLNCLLASTSPSSRRAFWWLVLAGWGLPVLFTGTWVSCKLAFEDIACWDLDDTSPYWWIIKGPIVLSVGVNFGLFLNIIRILVRKLEPAQGSLHTQSQYWRLSKSTLFLIPLFGIHYIIFNFLPDNAGLGIRLPLELGLGSFQGFIVAILYCFLNQEVRTEISRKW
>8097333_B8NBN5_4000755
PTNPLTLIVATTPIPTREKTLLGIGLNGTLPWPRIKADMSFFARVTTRPPRPGTTNAMIMGRKTYDSVPKSLRPLGKRINVIVTRDVEGVSKRVAEELKEKRAKMAAAAAAATSAGENKEEGPITDAIVSSGLEAALEDVEEKFKGGLGSVFVIGGAEIYATALGLGGDRPVRIVMTNVEKKGVDGEKAVFECDTFFPIDEELLMEKGWRKVSAEEVTEWVGEPVSGEWKDEGEVRIQMVGYERV
>8047374_P29033_4005615
DWGTLQTILGGVNKHSTSIGKIWLTVLFIFRIMILVVAAKEVWGDEQADFVCNTLQPGCKNVCYDHYFPISHIRLWALQLIFVSTPALLVAMHVAYRRHEKKRKFIKGEIKSEFKDIEEIKTQKVRIEGSLWWTYTSSIFFRVIFEAAFMYVFYVMYDGFSMQRLVKCNAWPCPNTVDCFVSRPTEKTVFTVFMIAVSGICILLNVTELCYLLIRY
>8022849_Q9I4A4_4000237
MASYAELFDIGEDFAAFVGHGLATEQGAVARFRQKLESNGLPSALTERLQRIERRYRLLVAGEMWCPDCQINLAALDFAQRLQPNIELAIISKGRAEDDLRQRLALERIAIPLVLVLDEEFNLLGRFVERPQAVLDGGPQALAAYKAGDYLEHAIGDVLAIIEGAA
>8022850_Q837R1_4000595
MDISVIDATKVNTETGLHIGESNAPVKMIEFINVRCPYCRKWFEESEELLAQSVKSGKVERIIKLFDKEKESLQRGNVMHHYIDYSAPEQALSALHKMFATQDEWGNLTLEEVATYAEKNLGLKEQKDATLVSAVIAEANAAHIQFVPTIIIGEYIFDESVTEEELRGYIEK
>8072809_A3DCZ0_4003632
AKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKKLLM
>8072799_A0A0H3AMJ9_4003632
NKNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGDFDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAATLKEKLDKIFE
如何使用上面的 fasta 数据这样的数据正确且无错误地创建blast数据库?
我有同样的错误,并且该命令仅在文件夹名称均不含空格时才有效。如果仍然不起作用,也许尝试重命名所有不带 _ 或任何其他非字母字符的文件夹