EDIT: solved. whilst I had properly defined the path to the NCBI executables in
I had not properly set the path in
It worked after I modified this second file. As I mention in comments below, just because the test files work fine, it doesn't mean your SIFT has properly been configured. When you read the output of the test files, all incorrect path/database configurations are ignored because the required database/protein alignment files are provided within the SIFT directory. I find this a bit misleading, but there we go. something to consider.
I cannot determine what is causing this however.
I am successfully using standalone SIFT. I can run SIFT using the test files provided:
$ csh bin/SIFT_for_submitting_fasta_seq.csh test/lacI.fasta db/uniref.fa test/lacI.subst tail is lacI.fasta query is /home/arron/Phd/programs/sift5.2.1/tmp/lacI.fasta.query /usr/share/ncbi-blast+/bin//bin//psiblast: Command not found. exiting because stauts not equal to 0 tell me i've entered info_on_seqs *** The following sequences have been removed because they were found to be over 100% identical with your protein query: *** The following sequences have been removed because they were found to be over 100% identical with your protein query: QUERY has 100 identity UniRef90_P03023Lacto has 100 identity UniRef90_A8AKB7Putat has 81 identity UniRef90_C1M7F8Lacre has 81 identity UniRef90_D2TK52Lacto has 78 identity UniRef90_E8XR69Trans has 59 identity UniRef90_D2C396Trans has 55 identity UniRef90_A9MQ83Putat has 76 identity UniRef90_C6DD30Trans has 53 identity UniRef90_E0SHJ3Trans has 56 identity UniRef90_D2ZG46Ribos has 54 identity UniRef90_C6CD23Trans has 51 identity UniRef90_A4W7D1Trans has 54 identity UniRef90_E8XW29Trans has 46 identity UniRef90_A1RAY2Trans has 38 identity UniRef90_D6DVN0Trans has 53 identity UniRef90_C4S4I8Lacto has 52 identity UniRef90_C9XUV2Lacto has 45 identity UniRef90_E3G6U0Trans has 54 identity UniRef90_C4UWB0Lacto has 52 identity UniRef90_C4UNI7Lacto has 48 identity UniRef90_D4GHV0LacIn has 50 identity UniRef90_C4TZY6Lacto has 50 identity UniRef90_D7CXK6Trans has 36 identity UniRef90_F0KTF2Lacre has 50 identity UniRef90_E1SIH9HTH-t has 50 identity UniRef90_D4E812LacIf has 44 identity UniRef90_D6YQA5HTH-t has 42 identity UniRef90_D5CE50Sugar has 43 identity UniRef90_C6CQF2Trans has 43 identity UniRef90_C4X4N1Trans has 43 identity UniRef90_A4TIF9Trans has 44 identity UniRef90_C4T764Lacto has 52 identity UniRef90_D1RRC7Trans has 41 identity UniRef90_E6WEY3Trans has 49 identity UniRef90_D8MUA6Lacto has 51 identity UniRef90_C9XWJ1Lacto has 45 identity UniRef90_D5CJ02Lacre has 54 identity UniRef90_D1RT73Trans has 43 identity UniRef90_P03023Lacto, UniRef90_P03023Lacto,. .<BR><BR> before seg fault? 9 10 13 14 15 16 18 19 20 21 22 23 25 30 34 45 50 53 56 65 76 127 166 179 187 188 197 201 205 218 220 241 247 249 250 252 256 272 274 284 286 288 326 356 357 358 359 360 filename is /home/arron/Phd/programs/sift5.2.1/blimps/docs/default.diri about to make predictions not including UniRef90_C4T764Lacto with X at 1 not including UniRef90_C4T764Lacto with X at 2 not including UniRef90_C4T764Lacto with X at 14 done checking all subst trying to free things here unalias: rm not found Output in /home/arron/Phd/programs/sift5.2.1/tmp/lacI.SIFTprediction
and produces a SIFT prediction file as expected.
However, when I try this with one of my own proteins of interest, the SIFT prediction file is not created.
$ csh bin/SIFT_for_submitting_fasta_seq.csh test/NP_000162.2.fasta db/uniref.fa test/glra1.subst tail is NP_000162.2.fasta query is /home/arron/Phd/programs/sift5.2.1/tmp/NP_000162.2.fasta.query /usr/share/ncbi-blast+/bin//bin//psiblast: Command not found. exiting because stauts not equal to 0 tell me i've entered info_on_seqs cannot open file /home/arron/Phd/programs/sift5.2.1/tmp/NP_000162.2.alignedfasta Output in /home/arron/Phd/programs/sift5.2.1/tmp/NP_000162.2.SIFTprediction
The clue here is in:
cannot open file /home/arron/Phd/programs/sift5.2.1/tmp/NP_000162.2.alignedfasta
where it appears an alignment via psiblast could not be made. I cannot find this file, but it should be produced.
how could this be??
For reference I include my
--1) test files (fasta and substitution file)
>gi|2506562|sp|P03023|LACI_ECOLI LACTOSE OPERON REPRESSOR MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS GLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQ QIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPT AMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ
--2) my protein files
>gi|119372310|ref|NP_000162.2| glycine receptor subunit alpha-1 isoform 2 precursor [Homo sapiens] MYSFNTLRLYLWETIVFFSLAASKEAEAARSAPKPMSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVSCN IFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYNEYPDDSLDLDPSMLDSIWKPDLFFANEKGAHFHEIT TDNKLLRISRNGNVLYSIRITLTLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQEQGAVQVADGL TLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWISFWINMDAAPAR VGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRQHKELLRFRRKRR HHKEDEAGEGRFNFSAYGMGPACLQAKDGISVKGANNSNTTNPPPAPSKSPEEMRKLFIQRAKKIDKISR IGFPMAFLIFNMFYWIIYKIVRREDVHNQ
any advice would be greatly appreciated.