Hi,
I’m having a very similar problem to rockx. I’m running mothur last version in Ubuntu. I want to run chimera.slayer, and I’ve installed blast (blast-2.2.16-ia32). I’m getting this:
mothur > chimera.slayer(fasta=STR_6743seqs_200511_core_blast_min700bp.align.fasta, template=/home/ramiro/Documents/DB/Biomarks/Laure/VersionFeb2011/Laure_DB_aligned/18S_1800_2000bp_Coreset_preliminar_Align_RL/18S_1800_2000bp_Coreset_preliminar_Align_12017seq_RL.fasta, processors=4)
Checking sequences from STR_6743seqs_200511_core_blast_min700bp.align.fasta …
Reading sequences from /home/ramiro/Documents/DB/Biomarks/Laure/VersionFeb2011/Laure_DB_aligned/18S_1800_2000bp_Coreset_preliminar_Align_RL/18S_1800_2000bp_Coreset_preliminar_Align_12017seq_RL.fasta…Done.
Only reporting sequence supported by 90% of bootstrapped results.
sh: Syntax error: end of file unexpected
Mothur won't quit, instead it keeps running at 100%, but nothing happens. Same input files with chimera.slayer in the previous version of Mothur works fine.
formatdb.log looks like this:
========================[ May 20, 2011 9:03 AM ]========================
Version 2.2.16 [Mar-25-2007]
Started database file “STR_6743seqs_200511_core_blast_min700bp.align.29317463.template.unaligned.fasta”
NOTE: CoreLib [002.003] FileOpen(".formatdbrc",“r”) failed
NOTE: CoreLib [002.003] FileOpen("/home/ramiro/.formatdbrc",“r”) failed
NOTE: [000.000] No number of link bits used found in config file. Ignoring
NOTE: [000.000] No number of membership bits used found in config file. Ignoring
Formatted 12017 sequences in volume 0
SUCCESS: formatted database STR_6743seqs_200511_core_blast_min700bp.align.29317463.template.unaligned.fasta
Any suggestions?
thanks!