makeblastdb issues

[Matthew Geniza]

command run:
transrate --threads 8 --assembly transcripts_CCDR_T0-output-v2-cdhitest --reference Oryza_sativa.IRGSP-1.0.cdna.all.fa

contig metrics are generated, but errors out when generating comparative metrics:

/local/cluster/transrate/lib/app/bin/transrate:13:in `raise': BLAST Error creating database: (RuntimeError)

USAGE
makeblastdb [-h] [-help] [-in input_file] [-input_type type]
-dbtype molecule_type [-title database_title] [-parse_seqids]
[-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
[-mask_desc mask_algo_descriptions] [-gi_mask]
[-gi_mask_name gi_based_mask_names] [-out database_name]
[-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
[-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.2.31+

Use '-help' to print detailed descriptions of command line arguments

Error: Too many positional arguments (1), the offending value: ./
from /local/cluster/transrate/lib/app/ruby/2.2.0/gems/crb-blast-0.6.6/lib/crb-blast/crb-blast.rb:119:in makedb' from /local/cluster/transrate/lib/app/ruby/2.2.0/gems/crb-blast-0.6.6/lib/crb-blast/crb-blast.rb:514:in run'
from /local/cluster/transrate/lib/app/lib/transrate/comparative_metrics.rb:154:in run_crb_blast' from /local/cluster/transrate/lib/app/lib/transrate/comparative_metrics.rb:23:in run'
from /local/cluster/transrate/lib/app/lib/transrate/transrater.rb:115:in comparative_metrics' from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:528:in comparative_metrics'
from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:405:in block in analyse_assembly' from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:400:in chdir'
from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:400:in analyse_assembly' from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:38:in block (2 levels) in run'
from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:37:in zip' from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:37:in block in run'
from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:32:in chdir' from /local/cluster/transrate/lib/app/lib/transrate/cmdline.rb:32:in run'
from /local/cluster/transrate/lib/app/bin/transrate:23:in `

'

[Rik]

how did you install transrate? It looks to me like transrate is trying to use a version of blast that you already have installed (2.3.31), rather than the one it needs (2.2.29)

You can either try transrate --install-deps or try the binary distribution of transrate from http://hibberdlab.com/transrate/installation.html

[Matthew Geniza]

Thanks for the reply, I work on a linux cluster -common tools like BLAST get updated regularly. a local copy of transrate was installed by downloading the linux binary, unpacking and adding the directory to the path. $transrate --install-deps ref Checking dependencies All dependencies installed Ill could try to install a local copy of 2.2.29, but a similar user had the same makeblastdb problem. They mentioned a workaround, but no final resolution was provided. https://groups.google.com/forum/#!topic/transrate-users/7QZ4EXyMFLY Is there a way to bypass the makeblastdb step and jump directly into the blast? standalone, the makeblastdb command works and generates the appropriate *nin, *nsq, and *nih. I could just move those to the appropriate transrate directory. On 4/5/17 9:42 AM, Richard Smith-Unna wrote:

…

how did you install transrate? It looks to me like transrate is trying to use a version of blast that you already have installed (|2.3.31|), rather than the one it needs (|2.2.29|) You can either try |transrate --install-deps| or try the binary distribution of transrate from http://hibberdlab.com/transrate/installation.html — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#207 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AT4VNP_ZbSilEYFbPXYrL97kA4_cj1xpks5rs8R2gaJpZM4MzpnO>.

[Rik]

Thanks for reporting this - it's actually a bug with how we load the dependencies in a rare case.

Do you have access to edit the /local/cluster/transrate/ file? Below I describe the fix depending on whether or not you can edit it:

If you can edit the file

replace the line:

export PATH=$SELFDIR/bin:$PATH

with:

export PATH=$SELFDIR/bin:$SELFDIR/lib/app/ruby/2.2.0/bin:$PATH

this will fix it for everyone who's using it

If you can't edit the file

when you run transrate, you'll have to run it like this:

PATH=/local/cluster/transrate/lib/app/ruby/2.2.0/bin:$PATH transrate

and put whatever arguments you wanted afterwards, e.g. in your example:

PATH=/local/cluster/transrate/lib/app/ruby/2.2.0/bin:$PATH transrate --threads 8 --assembly transcripts_CCDR_T0-output-v2-cdhitest --reference Oryza_sativa.IRGSP-1.0.cdna.all.fa

[Rik]

cc @cboursnell this is happening because bindeps installs to the GEM_HOME unless told otherwise or it can't find it: https://github.com/blahah/bindeps/blob/master/lib/bindeps.rb#L191.

We should either update the transrate wrapper bash script as above