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Old 04-24-2018, 11:29 AM   #1
Izal
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Location: Spain

Join Date: Jan 2018
Posts: 3
Exclamation InParanoid blastall and formatb ERROR

Hi everyone!

I'm trying to find protein orthologs between strains using InParanoid.
But when I execute it, I obtain errors in <formatdb> and <blast-all> phase.
Is this normal? Or am I doing something wrong? The command seems simple.
Thanks in advance!!!


Command:
$ perl inparanoid.pl strain1.fa strain2.fa

Here, a part of the Output with errors:
Trying to run BLAST now - this may take several hours ... or days in worst case!
Formatting BLAST databases
Done formatting
Starting BLAST searches...

Starting first BLAST pass for strain1.fa - strain1.fa on mar abr 24 20:53:57 CEST 2018
[blastall] WARNING: the -C 3 argument is currently experimental


Starting second BLAST pass for strain1.fa - strain1.fa on mar abr 24 20:54:38 CEST 2018
[formatdb] WARNING: Cannot add sequence number 1 (lcl|1_./tmpd) because it has zero-length.

[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
[blastall] FATAL ERROR: -triphosphate: Database ./tmpd was not found or does not exist

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.
[formatdb] WARNING: Cannot add sequence number 2 (lcl|2_./tmpd) because it has zero-length.

[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.
[blastall] FATAL ERROR: NZ_000411.1_prot_WP_011112711.1_1: Database ./tmpd was not found or does not exist
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Old 04-24-2018, 01:31 PM   #2
Izal
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Location: Spain

Join Date: Jan 2018
Posts: 3
Default

solved :-)
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