Help plz. Cannot get blastx XML output for analysis of de novo aphid transcriptome.

[matthew.christenson]

Hello,

I cannot seem to get blastx to run when the output format is XML. I need the blastx XML for to GO analysis using Blast2GO. The tabular format will be created when I enter the following commands but not the XML file:

blastx -query diaci_adult_transcriptome.fasta -db human_protein -out diaci_adult_v._human_blastx_e-3 -evalue .001 -max_target_seqs 2 -outfmt 6 -num_threads 20 -num_descriptions 1 -num_alignments 1 &

blastx -query diaci_adult_transcriptome.fasta -db human_protein -out diaci_adult_v_human_blastx_e-3_tab -evalue .001 outfmt 6 &

blastx -query diaci_adult_transcriptome.fasta -db human_protein -out diaci_adult_v._human_blastx_e-3 -evalue .001 -max_target_seqs 2 -outfmt 5 -num_threads 20 -num_descriptions 1 -num_alignments 1 &

blastx -query diaci_adult_transcriptome.fasta -db human_protein -out diaci_adult_v_human_blastx_e-3_tab -evalue .001 outfmt 5 &

Does anyone have the correct command or any suggestions?

Thank you very for your help.

[kmcarr]

In both of the commands you have shown you have directed BLASTX to output in tabular format (-outfmt 6) so it is behaving as expected. If you want XML output you need '-outfmt 5'.

[matthew.christenson]

Sorry, the commands were entered using both 6 (tabular) and 5 (XML). When I entered the command using 6, the output file is created, and the BLAST results began showing up in the tabular file. However, when I entered the command with 5, the output file was created and looking at top I can see the program is running, but no results are ever stored in the created XML file.

[amango]

Were you ever able to resolve this? I am having the same problem. Using blastx on my de novo assembly against the NCBI nr database (pre-formatted) yields an empty output file. When I run the same command but switch the output type to tab, it seems to work as expected. It would be nice to get the xml format.

xml command:
nohup blastx -db nr -query path_to_assembly/Ua_pn_300.fa -out Ua_pn_300_blastx -outfmt 5 &

tab command:
nohup blastx -db nr -query path_to_assembly/Ua_pn_300.fa -out Ua_pn_300_blastx_tab -outfmt 6 &

[matthew.christenson]

Yes, I foolishly didn't know that the BLAST program does not write to the XML files, unlike the tabular format, until the results from all of the sequences have been obtained. If you just let it go, it should eventually write to the files.

[BGould]

Same problem, ad hoc fix anyone?

Hi, I had the same problem. I completed a large blast run and now have a .dat file only. Does anyone have a way to generate an xml output file from the .dat file? I can't find this anywhere in the manual.

any help would be much appreciated!