Dear Peter, APOLOGIES for the delayed response Please see below for details...... On Thu, Aug 1, 2013 at 8:51 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I've seen that kind of error from NCBI BLAST+ before - do you know which of the BLAST tools was this, and what the query was?
The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus
The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser
OK, so this was a nucleotide FASTA file from an assembly, right?
Yes
What were you searching with BLAST? e.g. BLASTN against NT, BLASTX against NR, etc.
Search was blastn, task megablast of the assembly as query against an in-house made (and installed into galaxy) of a blastn database for Chromosomes 1 to 7 of Neurospora crassa Database was produced with: makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index and "installed" into the "blastdb.loc" file as required
Can you run this blastn search 'by hand' at the terminal?
Yes, yes and no
Does that crash too?
No and I do not know Please let me explain. I have set up the user galaxy account such that it has access to a directory called 'bioinfosoft' where all bioinformatics-related software is installed, including Blast+ Galaxy has 'access' to this directory and there I have compiled Blast+ 2.2.28+ Now, when I installed Blast+ via the toolshed, the toolshed Blast+ package did download and install what I believe it was the 2.2.26+ version of Blast+? If I recall correctly, I got an error message that went away while the Blast+ package was being compiled by the toolshed The errors I got running Blast did all occur when using that particular version of Blast+ (2.2.26) I then removed or uninstalled the packaged and tried to re-install again, but, as I said, it hanged there forever, installing... To my surprise when I re-run the jobs, they all worked well. This is, Blast worked like a charm BUT it did because it is NOT using the Blast packaged that was installed by the toolshed but the Blast package I compiled myself (2.2.28+) (SEE LOG AT END OF THIS MESSAGE...) Comparing the directory of galaxy with those of my backups I can see that the packaged Blast 2.2.26+ that was installed by the toolshed in the directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ is no longer there.. The directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/ is present but it is empty Therefore to answer your questions:
Can you run this blastn search 'by hand' at the terminal?
Yes, I can but I would be using a different version of Blast+
Does that crash too?
No, because I would be using a different version of Blast+
The error sounds very similar to this report which turned out to be due to a corrupted BLAST database - so also try recreating your DB: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962
Regarding this last comment..basically a corrupt database is not the problem in this case as demonstrated by the fact that I can run Blast on those databases Having said that, yes I have observed that depending on how one runs the makeblastdb command and depending on the type of fasta files used, you can end up with corrupt output. Some identifiers and symbols present in the fasta ID can interfere with makeblastdb (especially some produced by the JGI) In summary, yes Blast+ is working but because is not using the compiled Blast+ binaries installed by the toolshed package The problem I have is that I would like to be able to properly uninstall and re-install the Blast+ toolsheed so that things work as they were originally supossed to On the other hand, if you guys upgrade the package, this might be a non-issue as the toolshed would just simply generate new directories... Last, I noticed the command used in the compilation is different from the one I normally use The command I use is: tar -xzvf ncbi-blast-2.2.28+-src.tar.gz cd ncbi-blast-2.2.28+-src/c++ ./configure --prefix=/usr/local/galaxy/bioinfosoft/blast-2.2.28+ --with-64 --with-bincopy --with-mt --without-debug --with-static | tee c.log make | tee m.log make check make install Many Thanks --Rodolfo
Peter
LOG: galaxy.jobs.handler INFO 2013-08-05 12:11:30,841 (2405) Job dispatched galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blastn' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blastn', ignoring galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blast+' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blast+', ignoring galaxy.jobs.runners.local DEBUG 2013-08-05 12:11:31,099 (2405) executing: blastn -version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_2405; blastn -query "/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2897.dat" -db "/data/db/fungidb/Ncrassa_OR74A/blastplus_db/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" -task megablast -evalue 0.001 -out "/usr/local/galaxy/galaxy-dist/database/files/003/dataset_3596.dat" -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8 galaxy.jobs DEBUG 2013-08-05 12:11:31,152 (2405) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-08-05 12:11:32,230 execution finished: blastn -version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_2405; blastn -query "/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2897.dat" -db "/data/db/fungidb/Ncrassa_OR74A/blastplus_db/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" -task megablast -evalue 0.001 -out "/usr/local/galaxy/galaxy-dist/database/files/003/dataset_3596.dat" -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8 galaxy.jobs.runners DEBUG 2013-08-05 12:11:32,324 executing external set_meta script for job 2405: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmp7F7qqE /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_in_HistoryDatasetAssociation_4245_qhcDd5,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_kwds_HistoryDatasetAssociation_4245_pKXnUR,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_out_HistoryDatasetAssociation_4245_jSXP0f,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_results_HistoryDatasetAssociation_4245_WzHo1J,,/usr/local/ galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_override_HistoryDatasetAssociation_4245_OBr8F0 galaxy.jobs.runners DEBUG 2013-08-05 12:11:33,882 execution of external set_meta for job 2405 finished