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Error while using MPI-BLAST

I installed MPI-BLAST in linux (ubuntu 16.04) , but while running query its generates an error, which may be pointed towards DATABASE.

to create database i ran this query:

$mpiformatdb -N 16 -i /home/ntm/Downloads/MPI_BLAST_MTB_ASM/all_ASM.fna -o /home/ntm/mpiblast/mtb_ASM

result was:

Reading input file

111Done, read 86563441 lines

Database type unspecified, assuming nucleotide

Breaking all_ASM.fna into 16 fragments

Executing: formatdb -i /home/ntm/Downloads/MPI_BLAST_MTB_ASM/all_ASM.fna -p F -N 16 -o T 

Created 16 fragments.

<<< Please make sure the formatted database fragments are placed in /home/ntm/mpiblast/ before executing mpiblast. >>>

i ran this query:

$mpiexec -n 18 mpiblast -p blastn -d mpiblast/all.fna -i /home/ntm/samples/test_data/100/100.fasta -o /home/ntm/samples/test_data/100/r_100.txt

and get this error:

Error opening /home/ntm/mpiblast/mpiblast/all.fna.mbf

open: No such file or directory

Fatal Error:

Unable to access fragment list file

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 17 in communicator MPI_COMM_WORLD 
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------

4   0.00846505  Bailing out with signal 15

5   0.0102329   Bailing out with signal 15

6   0.023458            Bailing out with signal 15

7   0.0255911   Bailing out with signal 15

8   0.032532            Bailing out with signal 15

9   0.03491         Bailing out with signal 15

10  0.035645            Bailing out with signal 15

11  0.0363281   Bailing out with signal 15

12  0.038064            Bailing out with signal 15

13  0.039439            Bailing out with signal 15

14  0.0391941   Bailing out with signal 15

15  0.0411971   Bailing out with signal 15

16  0.0412331   Bailing out with signal 15

0   0.00338316  Bailing out with signal 15

1   0.00537801  Bailing out with signal 15

2   0.00614786  Bailing out with signal 15

3   0.00781703  Bailing out with signal 15

[ablab:06080] 17 more processes have sent help message help-mpi-api.txt / mpi-abort

[ablab:06080] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

how can i remove this error?

genome alignment sequencing software error

Hello genious.kalia.141198,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

Have you done this part?

Please make sure the formatted database fragments are placed in /home/ntm/mpiblast/ before executing mpiblast.

yes, i did. just after my formatted database get ready i copied all the files to the location you mentioned.

Is /home/ntm/mpiblast/mpiblast/all.fna.mbf present and readable from all nodes? The error say that the file could not be read.

yeah, i resolved this.. but MPI-BLAST still generating errors.

mpiexec -n 3 mpiblast -p blastn -d mpiblast/all_ASM.fna -i /home/ntm/samples/test_data/100/100.fasta -o /home/ntm/samples/test_data/100/r_100.txt

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fnaABL4KB.nin

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin

[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fnaABL4KB.nin

[blastall] FATAL ERROR: NZ_CP009614.1_0000000001: Database /home/ntm/mpiblast/mpiblast /all_ASM.fnaABL4KB was not found or does not exist

1 0.052954 Bailing out with signal -1


MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.


2 0.054822 Bailing out with signal 15

0 0.0540459 Bailing out with signal 15

[ablab:17905] 2 more processes have sent help message help-mpi-api.txt / mpi-abort

[ablab:17905] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

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