rBLAST
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mhahsler
No results with test data set.
Hello, Thank you for this super useful package. While I had success installing the package, when run the test data set, Blast does not return matches. I have a similar result when I try running another sequence I know should have a match. My error message is "BLAST did not return a match!" (screen shot below). I would greatly appreciate any advice in beginning to trouble shoot this.
My session information: R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS 10.16
Matrix products: default BLAS/LAPACK: /Users/amyvandiver/opt/anaconda3/envs/r_n1/lib/libopenblasp-r0.3.12.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages:
[1] ggplot2_3.3.5 GenomicAlignments_1.26.0
[3] Rsamtools_2.6.0 SummarizedExperiment_1.20.0
[5] Biobase_2.50.0 MatrixGenerics_1.2.1
[7] matrixStats_0.61.0 GenomicRanges_1.42.0
[9] GenomeInfoDb_1.26.7 rBLAST_0.99.2
[11] Biostrings_2.58.0 XVector_0.30.0
[13] IRanges_2.24.1 S4Vectors_0.28.1
[15] BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] pbdZMQ_0.3-7 repr_1.1.4 lattice_0.20-45
[4] colorspace_2.0-3 vctrs_0.3.8 htmltools_0.5.2
[7] base64enc_0.1-3 utf8_1.2.2 rlang_1.0.1
[10] pillar_1.7.0 glue_1.6.1 withr_2.4.3
[13] BiocParallel_1.24.1 RColorBrewer_1.1-2 uuid_1.0-3
[16] plyr_1.8.6 GenomeInfoDbData_1.2.4 lifecycle_1.0.1
[19] zlibbioc_1.36.0 munsell_0.5.0 gtable_0.3.0
[22] evaluate_0.15 fastmap_1.1.0 fansi_1.0.2
[25] Rcpp_1.0.8 IRdisplay_1.1 scales_1.1.1
[28] BiocManager_1.30.16 IRkernel_1.3 DelayedArray_0.16.3
[31] jsonlite_1.8.0 digest_0.6.29 grid_4.0.2
[34] tools_4.0.2 bitops_1.0-7 magrittr_2.0.2
[37] RCurl_1.98-1.6 tibble_3.1.6 crayon_1.5.0
[40] pkgconfig_2.0.3 ellipsis_0.3.2 Matrix_1.4-0
[43] R6_2.5.1 compiler_4.0.2
Hi, I think reading the output of BLAST somehow fails on your system. I have changed the code so it used system2() and reports errors while reading the BLAST output. Please update the package from GitHub and try again.
Thank you very much!
On Thu, Feb 24, 2022 at 11:54 AM Michael Hahsler @.***> wrote:
Hi, I think reading the output of BLAST somehow fails on your system. I have changed the code so it used system2() and reports errors while reading the BLAST output. Please update the package from GitHub and try again.
— Reply to this email directly, view it on GitHub https://github.com/mhahsler/rBLAST/issues/23#issuecomment-1050209236, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQWUS4VZUAXD4WGWI5HGSTU42EJFANCNFSM5PF4LEHA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Hi,
similarly thanks for the the cool package! I could successfully install it after installing in my linux ncbi-blast+ with
sudo apt install ncbi-blast+
which installed the 2.9.0 version.
> system("blastn -version")
blastn: 2.9.0+
Package: blast 2.9.0, build Sep 30 2019 01:57:31
After setting the database as per instructions it seems all ok
> bl
BLAST Database
Location: /home/dibrab/Dropbox/R_scripts/ALEJ/16SMicrobialDB/16S_ribosomal_RNA
BLAST Type: blastn
Database: 16S ribosomal RNA (Bacteria and Archaea type strains)
23,104 sequences; 33,530,608 total bases
Date: Oct 1, 2022 5:36 AM Longest sequence: 3,600 bases
BLASTDB Version: 5
Volumes:
/home/dibrab/Dropbox/R_scripts/ALEJ/16SMicrobialDB/16S_ribosomal_RNA
However when trying the prediction I get the following message
Error: NCBI C++ Exception:
T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/objistrasnb.cpp", line 499: Error: byte 96: overflow error ( at [].[].gi)
T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/member.cpp", line 769: Error: ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)
Error in read.table(outfile, sep = ",", quote = "") :
no lines available in input
Warning message:
In predict.BLAST(bl, seq[1, ]) : BLAST did not return a match!
It seems that it has issues while reading the output. Might it depend on the blast+ version? thanks a lot
The error comes from the blast executable.
Google says that the reason is an incompatible blast version: https://stackoverflow.com/questions/70370949/local-blast-ncbi-c-exception