Comments (6)
DomBennett
commented on July 20, 2024
Hi @naupaka!
Thanks for spending so much time on reviewing the phylotaR code. I'm trying to work out why you were getting the makeblstdb error. Would it be possible for you to send me the BLAST log files? They should be in [wd]/blast/[unique-name]-db.log.
Thanks!
Dom
from phylotar.
naupaka
commented on July 20, 2024
@DomBennett my suspicion is that is has something to do with the wd path not being parsed properly somewhere along the line.
Here's one log:
BLAST options error: File ~/Desktop/phylota_review/capnodiales/blast/taxon-1047167-typ-subtree-db.fa does not exist
w/capnodiales/blast/taxon-1047167-typ-subtree-db.fa
New DB title: ~/Desktop/phylota_review/capnodiales/blast/taxon-1047167-typ-subtree-db.fa
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
and another:
BLAST options error: File ~/Desktop/phylota_review/fungi/blast/taxon-41254-typ-subtree-db.fa does not exist
ta_review/fungi/blast/taxon-41254-typ-subtree-db.fa
New DB title: ~/Desktop/phylota_review/fungi/blast/taxon-41254-typ-subtree-db.fa
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
There doesn't seem to be a BLAST log for the last example ("aotus").
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naupaka
commented on July 20, 2024
Huh. Now it seems to work fine. Not sure what changed.
> library(phylotaR)
> txid <- 9504
> setUp(wd="/Users/naupaka/Desktop/phylota_review/aotus", txid=txid, ncbi_dr=ncbi_dr, v=TRUE)
-----------------------------------------------
phylotaR: Implementation of PhyLoTa in R [v0.1]
-----------------------------------------------
Checking for valid NCBI BLAST+ Tools ...
Error in file.path(d, "makeblastdb") : object 'ncbi_dr' not found
> ncbi_dr <- "/usr/local/bin"
> setUp(wd="/Users/naupaka/Desktop/phylota_review/aotus", txid=txid, ncbi_dr=ncbi_dr, v=TRUE)
-----------------------------------------------
phylotaR: Implementation of PhyLoTa in R [v0.1]
-----------------------------------------------
Checking for valid NCBI BLAST+ Tools ...
Found: [/usr/local/bin/makeblastdb]
Found: [/usr/local/bin/blastn]
Setting up pipeline with the following parameters:
. blstn [/usr/local/bin/blastn]
. btchsz [300]
. date [2018-04-04]
. mdlthrs [3000]
. mkblstdb [/usr/local/bin/makeblastdb]
. mncvrg [51]
. mnsql [250]
. mxevl [1e-10]
. mxnds [1e+05]
. mxrtry [100]
. mxsql [2000]
. mxsqs [50000]
. ncps [1]
. txid [9504]
. v [TRUE]
. wd [/Users/naupaka/Desktop/phylota_review/aotus]
Error in setUpCch(ps = ps) : Cache already exists, ovrwrt=FALSE.
> restart(wd="/Users/naupaka/Desktop/phylota_review/aotus")
------------------------------------------------------
Restarting pipeline on [unix] at [2018-04-04 09:54:00]
------------------------------------------------------
Running stages: taxise, download, cluster, cluster2
--------------------------------------------
Starting stage TAXISE: [2018-04-04 09:54:00]
--------------------------------------------
Searching taxonomic IDs ...
Downloading taxonomic records ...
. [1-21]
Generating taxonomic dictionary ...
---------------------------------------------
Completed stage TAXISE: [2018-04-04 09:54:03]
---------------------------------------------
----------------------------------------------
Starting stage DOWNLOAD: [2018-04-04 09:54:03]
----------------------------------------------
Identifying suitable clades ...
Identified [1] suitable clades.
Downloading hierarchically ...
Working on parent [id 9504]: [1/1] ...
. + whole subtree ...
. . Getting [2805 sqs] ...
. . . [1-300]
. . . [301-600]
. . . [601-900]
. . . [901-1200]
. . . [1201-1500]
. . . [1501-1800]
. . . [1801-2100]
. . . [2101-2400]
. . . [2401-2700]
. . . [2701-2805]
Successfully downloaded [2980 sqs] in total.
-----------------------------------------------
Completed stage DOWNLOAD: [2018-04-04 09:55:48]
-----------------------------------------------
---------------------------------------------
Starting stage CLUSTER: [2018-04-04 09:55:48]
---------------------------------------------
Working on [id 9504]
. Generating subtree clusters for [id 9504(genus)]
. Generating direct clusters for [id 9504(genus)]
. . [0 sqs]
. . . Too few sequences, cannot make clusters
. BLASTing [2980 sqs] ....
. . Running makeblastdb
. . Running blastn
. . Removed [17762/90442] BLAST hits due to insufficient coverage
. Identified [837] clusters
. Processing [id 9504] child [id 1263727]
. . Generating subtree clusters for [id 1263727(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 1230482]
. . Generating subtree clusters for [id 1230482(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 1090913]
. . Generating subtree clusters for [id 1090913(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 1002694]
. . Generating subtree clusters for [id 1002694(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 940829]
. . Generating subtree clusters for [id 940829(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 413234]
. . Generating subtree clusters for [id 413234(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 361674]
. . Generating subtree clusters for [id 361674(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 292213]
. . Generating subtree clusters for [id 292213(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 261316]
. . Generating subtree clusters for [id 261316(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 231953]
. . Generating subtree clusters for [id 231953(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 222417]
. . Generating subtree clusters for [id 222417(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 57176]
. . Generating subtree clusters for [id 57176(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 57175]
. . Generating subtree clusters for [id 57175(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 43147]
. . Generating subtree clusters for [id 43147(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 37293]
. . Generating subtree clusters for [id 37293(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 30591]
. . Generating subtree clusters for [id 30591(species)]
. . Generating direct clusters for [id 30591(species)]
. . . [507 sqs]
. . BLASTing [507 sqs] ....
. . Removed [141/4130] BLAST hits due to insufficient coverage
. . Identified [253] clusters
. . BLASTing [244 sqs] ....
. . Removed [176/2300] BLAST hits due to insufficient coverage
. . Identified [85] clusters
. . Processing [id 30591] child [id 867331]
. . . Generating subtree clusters for [id 867331(subspecies)]
. . . . . [0 sqs] -- too few sequences, cannot make clusters
. . Processing [id 30591] child [id 280755]
. . . Generating subtree clusters for [id 280755(subspecies)]
. . . . . [0 sqs] -- too few sequences, cannot make clusters
. . Processing [id 30591] child [id 120088]
. . . Generating subtree clusters for [id 120088(subspecies)]
. . . . . [0 sqs] -- too few sequences, cannot make clusters
. Processing [id 9504] child [id 9505]
. . Generating subtree clusters for [id 9505(species)]
. . . . [0 sqs] -- too few sequences, cannot make clusters
[1/1]
----------------------------------------------
Completed stage CLUSTER: [2018-04-04 09:56:03]
----------------------------------------------
-----------------------------------------------
Starting stage CLUSTER^2: [2018-04-04 09:56:03]
-----------------------------------------------
Loading clusters ...
Done. Only one cluster set -- skipping cluster^2
Dropping all clusters of < 3 sqs ...
Renumbering clusters ...
Saving ...
------------------------------------------------
Completed stage CLUSTER^2: [2018-04-04 09:56:03]
------------------------------------------------
-------------------------------------------
Completed pipeline at [2018-04-04 09:56:03]
-------------------------------------------
> devtools::session_info()
Session info ---------------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.4 (2018-03-15)
system x86_64, darwin17.3.0
ui RStudio (1.1.383)
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-04-04
Packages -------------------------------------------------------------------------------------------------------------------
package * version date source
base * 3.4.4 2018-03-15 local
compiler 3.4.4 2018-03-15 local
curl 3.1 2017-12-12 CRAN (R 3.4.3)
datasets * 3.4.4 2018-03-15 local
devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
graphics * 3.4.4 2018-03-15 local
grDevices * 3.4.4 2018-03-15 local
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
igraph 1.2.1 2018-03-10 CRAN (R 3.4.3)
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.4 2018-03-15 local
phylotaR * 0.1 2018-03-26 Github (DomBennett/phylotaR@2541b03)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.4.1)
R.oo 1.21.0 2016-11-01 CRAN (R 3.4.1)
R.utils 2.6.0 2017-11-05 CRAN (R 3.4.2)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
rentrez 1.2.1 2018-03-05 CRAN (R 3.4.3)
stats * 3.4.4 2018-03-15 local
sys 1.5 2017-10-10 cran (@1.5)
tools 3.4.4 2018-03-15 local
treeman 1.1.1 2017-06-27 cran (@1.1.1)
utils * 3.4.4 2018-03-15 local
withr 2.1.2 2018-03-15 CRAN (R 3.4.3)
XML 3.98-1.10 2018-02-19 CRAN (R 3.4.3)
yaml 2.1.18 2018-03-08 CRAN (R 3.4.3)
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin17.3.0 (64-bit)
Running under: macOS High Sierra 10.13.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] phylotaR_0.1
loaded via a namespace (and not attached):
[1] XML_3.98-1.10 treeman_1.1.1 withr_2.1.2 digest_0.6.15 R.methodsS3_1.7.1 R6_2.2.2
[7] sys_1.5 jsonlite_1.5 magrittr_1.5 httr_1.3.1 curl_3.1 rstudioapi_0.7
[13] rentrez_1.2.1 R.oo_1.21.0 R.utils_2.6.0 devtools_1.13.5 tools_3.4.4 igraph_1.2.1
[19] yaml_2.1.18 compiler_3.4.4 pkgconfig_2.0.1 memoise_1.1.0 from phylotar.
naupaka
commented on July 20, 2024
The only other thing that's different is that this time I used the stable version of RStudio, whereas usually I use the daily build.
from phylotar.
DomBennett
commented on July 20, 2024
The only thing I was thinking is it might be to do with ~/ which isn't rendered properly when called outside R through the sys package. But it seemed as if you specifically tested for that in your review.
At the very least, I should prevent users using the ~/.
from phylotar.
DomBennett
commented on July 20, 2024
Now preventing users run with ~ in filepaths.
from phylotar.
Related Issues (20)
- problem with the restez/phylota integration
- Possibility to supply NCBI API key when running pipeline to access NCBI data faster? HOT 1
- Use phylotaR for retrieving orthologous protein sequences HOT 1
- No periods or tildes in file paths HOT 3
- Multiple markers/loci per cluster issue HOT 4
- Can not install the package in windows HOT 2
- Clusters with different parent number but the same MAD, seed, length, n_taxa, n_seqs
- Description - not enough information
- New Maintainer Wanted HOT 5
- Next release HOT 6
- CRAN archive of package outsider
- Fix pkgdown configuration for reference HOT 3
- No need for restez_connect() HOT 1
- Remove treeman as a dependency? HOT 2
- Could get something new from https://github.com/pachterlab/gget
- test failure HOT 1
- Generating taxonomic dictionary error HOT 1
- Fetch and error seem to be stuck HOT 2
- drop taxa functionality HOT 1
- Identical clusters making it into alignments HOT 1
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