Blank file with identify_chimeric_sequences.py script, blast fragments method

[Rachel C.]

When I try to run the script, I get a blank chimeric_seqs_blast.txt output file and no error messages in the terminal

 The following is my script:

identify_chimeric_seqs.py -i /Users/r**/Documents/BaseSpaceData/RachelsData/aligned_seqs/rep_set.fna -t /Users/r**/Documents/BaseSpaceDataDupe/All_FastQ_files/sh_qiime_release_01.08.2015/sh_taxonomy_qiime_ver7_97_01.08.2015.txt -r /Users/r**/Documents/BaseSpaceDataDupe/All_FastQ_files/sh_qiime_release_01.08.2015/sh_refs_qiime_ver7_97_01.08.2015.fasta -m blast_fragments -o /Users/r**/Documents/BaseSpaceData/RachelsData/aligned_seqs/chimeric_seqs_blast.txt

(this is on ITS data)

I have looked at a few similar questions, many of the people seem to have their issue solved by listing the full file path for each file, but I am still getting a blank file

I ran this script:

print_qiime_config.py -tf

And did not see errors related to blast (ChimeraSlayer has an error but I am not using that method for ITS)

Any help would be appreciated

Thanks,

Rachel

[Embriette]

Hi Rachel,

Can you please send your log file? Are there any error messages resulting from running the command? Is the command is done running? You may see an empty file if the process is still working or is hanging. 

In the meantime, reading through the documentation for identify_chimeric_seqs.py, I think that what you are seeing could be due to the nature of the way blast_fragments works (if everything else looks ok in your log file). It works both by splitting sequences into fragments, and by taking into account taxonomy assignment and depth (looks like you used the default of 4, which would be order level). I would recommend reading the documentation carefully and adjusting your command as needed-perhaps you could try setting a deeper taxonomy level?

Best,

Embriette