Problem running Fastortho Debian 8.7
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4.5 years ago

Hello everyone.

i was trying to carry out an orthologous finding analysis with FastOrtho following this structure https://github.com/grovesdixon/using_FastOrtho/blob/master/fastOrtho_local_WALKTHROUGH.txt. When run the the program

In the terminal:

makeblastdb -dbtype prot -in /home/FastOrtho/workind_dir/test1_out/test1.faa
                     Building a new DB, current time: 05/22/2017 13:19:22

blastp -db /home/FastOrtho/workind_dir/test1_out/test1.faa -query /home/FastOrtho/workind_dir/test1_out/test1.faa -evalue 1e-5 -num_threads 1 -num_descriptions 11 -num_alignments 10 -out /home/FastOrtho/workind_dir/test1_out/test1.out -outfmt 6
Warning: The parameter -num_descriptions is ignored for output formats > 4 .


Use -max_target_seqs to control output
 0.00 to classify blast hits

Segmentation falt

I don't know how to do that change -num_descriptions to -max_target_seqs because is an internal blastp confution. in the other hand, i didn't find a command provided by FastOrtho tool to solve this problem.

.

My architecture and version is: 64bit, SO: Debian 8.7; makeblastdb: 2.2.29+, blastp: 2.2.29+, mcl 14-137 (looks like the version name)

Many help we really apreciate.

Fastortho orthologous • 1.8k views
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Have you tested ORTHO install as described in the file you linked?

You are using an old install of BLAST+ (that was current in Jan 2014). So I suggest you try upgrading that.

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Hi, first of all thanks for reply and sorry for the delay in answering. i've follow the ortho install described in the link, even with the same issue described in that link. in the other side, I have upgraded BLAST+ to the last version 2.6.0+ , but i couldn't do the test right now to be sure if that solve the problem, because i must wait for another blast run. i guess today finish to do the test.

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Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

Testing ORTHO install would not solve a problem (if one exists) but it will tell you if the install is otherwise correct and working as expected.

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Sorry about the delay in responding. i have testing fastortho with 2 fasta files and get the following issue:

 ./FastOrtho --option_file ../workind_dir/options.txt 

makeblastdb -dbtype prot -in /home/ricardo/Documentos/SW/FastOrtho/workind_dir/test1_out/test1.faa


Building a new DB, current time: 06/02/2017 10:20:42

New DB name:   /home/ricardo/Documentos/SW/FastOrtho/workind_dir/test1_out/test1.faa

New DB title:  /home/ricardo/Documentos/SW/FastOrtho/workind_dir/test1_out/test1.faa

Sequence type: Protein

Keep MBits: T

Maximum file size: 1000000000B

Adding sequences from FASTA; added 22 sequences in 0.00213385 seconds.

blastp -db SW/FastOrtho/workind_dir/test1_out/test1.faa -query SW/FastOrtho/workind_dir/test1_out/test1.faa -evalue 1e-5 -num_threads 1 -num_descriptions 50 -num_alignments 50 -out SW/FastOrtho/workind_dir/test1_out/test1.out -outfmt 6

Warning: [blastp] The parameter -num_descriptions is ignored for output formats > 4 . 

Use -max_target_seqs to control output
 0.00 to classify blast hits

ViolaciĆ³n de segmento

2 things : 1.- I don't know how to set a parameter to blastp read the -num_descriptions command, in the fastortho manual doesn't exist that option to add it in the opt.txt file. 2.- The cant handle the "violacion de segmento" (segmentation fault), i guess it is happening due to the previous issue, but how to fix it??...

if you know what is the parameter or what else i'll really appreciate.

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Did you get the correct blast+ executable for your OS or compile it from source? I don't think the seg fault is occuring because of #1. That is just a warning.

Are you able to successfully run a blastp search directly (outside ORTHO)?

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hi thank for reply As the first step to get blastp, i installed from apt-get terminal blast and their tools(blastp,blastx ....), and then to updgraded blast+ download File:ncbi-blast-2.6.0+-x64-linux.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ . i have runned blastp against differents db whit my own dataset with no problem.

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I am not sure what to tell you next. Clearly your blast install seems to be working (can you check by running blastp -h to make sure you are getting the new version of blast+ by default) and the problem must thus be on the ORTHO side.

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i have tiped blastp -h and get the usage information and "DESCRIPTION Protein-Protein BLAST 2.6.0+" , so i guess the new version of blastp it is working.

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