Shortbred Identify BLAST database error

[Violetta Florova]

Hello,

I'm trying to create new markers from ADRB 2019 blasting against uniref90

Would you think this error relates to the problem with the local python version or  uniref version or ...?

Making BLAST database for the family consensus sequences... Making BLAST database for the reference protein sequences... Checking dependencies... Checking to make sure that installed version of usearch can make databases... Traceback (most recent call last): File "./shortbred_identify.py", line 299, in <module> "-dbtype", "prot", "-logfile", dirTmp + os.sep + "refdb.log"]) File "/util/academic/python/anaconda2-4.3.1/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['makeblastdb', '-in', 'uniref90.fasta', '-out', 'tmp2996901560013745059/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp2996901560013745059/refdb.log']' returned non-zero exit status -24

This is the text from refdb.log file:

Building a new DB, current time: 06/08/2019 13:09:36 New DB name: /projects/academic/mjbuck/Buck_Lab_Members/violetta/project1/shortbred/tmp2996901560013745059/refdb/refdb New DB title: uniref90.fasta Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B

THANK YOU!

[Eric Franzosa]

Hmm, hard to say from this message, other than that the blast database indexing failed. You can try running that command outside of ShortBRED and see if the same thing happens:

makeblastdb -in uniref90.fasta -out uniref90.db -dbtype prot -logfile uniref90.log

Thanks,

Eric

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[Violetta Florova]

Thank you so much.

I was able to run makeblastdb, but unfortunately, when I run the adjusted_ADRB2019.fasta against uniref90.fasta (the size of unref90.fasta is around 20GB), it takes more than 72 hours to finish. 

Is it correct time? It worked good with the test reference database. 

Thank you,

Violetta

On Tuesday, June 11, 2019 at 12:46:46 PM UTC-4, Eric Franzosa wrote:

Hmm, hard to say from this message, other than that the blast database indexing failed. You can try running that command outside of ShortBRED and see if the same thing happens:

makeblastdb -in uniref90.fasta -out uniref90.db -dbtype prot -logfile uniref90.log

Thanks,

Eric

On Sat, Jun 8, 2019 at 3:39 PM Violetta Florova <florova...@gmail.com> wrote:

Hello,

I'm trying to create new markers from ADRB 2019 blasting against uniref90

Would you think this error relates to the problem with the local python version or  uniref version or ...?

Making BLAST database for the family consensus sequences... Making BLAST database for the reference protein sequences... Checking dependencies... Checking to make sure that installed version of usearch can make databases... Traceback (most recent call last): File "./shortbred_identify.py", line 299, in <module> "-dbtype", "prot", "-logfile", dirTmp + os.sep + "refdb.log"]) File "/util/academic/python/anaconda2-4.3.1/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['makeblastdb', '-in', 'uniref90.fasta', '-out', 'tmp2996901560013745059/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp2996901560013745059/refdb.log']' returned non-zero exit status -24

This is the text from refdb.log file:

Building a new DB, current time: 06/08/2019 13:09:36 New DB name: /projects/academic/mjbuck/Buck_Lab_Members/violetta/project1/shortbred/tmp2996901560013745059/refdb/refdb New DB title: uniref90.fasta Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B

THANK YOU!

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[Violetta Florova]

I'm really sorry, I can't find why the code keeps crashing. 

It work good when I use "ref_prots,faa" as the reference database, but it doesn't run with uniref90 database.

Traceback (most recent call last): File "./shortbred_identify.py", line 299, in <module> "-dbtype", "prot", "-logfile", dirTmp + os.sep + "refdb.log"]) File "/util/academic/biopython/1.70/anaconda-5.0.1/lib/python2.7/subprocess.py", line 186, in check_call

raise CalledProcessError(retcode, cmd) 

d)
subprocess.CalledProcessError: Command '['/projects/academic/mjbuck/Buck_Lab_Members/violetta/project1/shortbred/ncbi-blast-2.9.0+/bin/makeblastdb', '-in', 'uniref90_adj.fasta', '-out', 'tmp217051562087438433/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp217051562087438433/refdb.log']' returned non-zero exit status -24

  File "./shortbred_identify.py", line 299, in <module>
    "-dbtype", "prot", "-logfile", dirTmp + os.sep +  "refdb.log"])
  File "/util/academic/biopython/1.70/anaconda-5.0.1/lib/python2.7/subprocess.py", line 186, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/projects/academic/mjbuck/Buck_Lab_Members/violetta/project1/shortbred/ncbi-blast-2.9.0+/bin/makeblastdb', '-in', 'uniref90_adj.fasta', '-out', 'tmp217051562087438433/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp217051562087438433/refdb.log']' returned non-zero exit status -24