Diamond allignment tool error.

Question

[faizansaleem1992]

Hello!

I have been using diamond for the blastx purpose and it works perfectly but recently an error has occured and I dont know how to resolve it. following is the command I used:

Diamond$ ./diamond blastx -d nr -q saiful_1.fq -o saiful_1_nr_diamond.m8 --more-sensitive -b 1 -f 6 qgi sgi qseqid sseqid qlen slen qstart qend sstart send length qcovs pident evalue stitle

The error that occurred was:

Joining output blocks... Error: Invalid output field Error: Invalid output field terminate called recursively Error: Invalid output field terminate called recursively Error: Invalid output field terminate called recursively Aborted (core dumped)

Kindly help I will be very much thankful to you.

Best Regards, Faizan Saleem

[jonasmst]

Looking at the source code, the error message seems to be related to the fields you've specified at the end of the command, i.e. qgi sgi qseqid sseqid qlen slen qstart qend sstart send length qcovs pident evalue stitle, and that one of them causes an error since it doesn't recognize the keyword. However, to me it looks like you've spelled them correctly. Perhaps try running it again without specifying keywords, just with ./diamond blastx -d nr -q saiful_1.fq -o saiful_1_nr_diamond.m8 --more-sensitive -b 1 -f 6 to see if it runs without issues. Some fields are included by default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore. I'd try with the default values (providing no keywords) and see if it works then. If it doesn't, it looks to me as if there's a bug in the code.

Answer 1

[jtclaypo]

Working through this problem today and it looks as "qcovs" is not specified within Diamond. For any future users that run into this, that was my fix. "qcovhsp" is however supported if you want. So try

diamond blastx -d nr -q saiful_1.fq -o saiful_1_nr_diamond.m8 --more-sensitive -b 1 \
  -f 6 qgi sgi qseqid sseqid qlen slen qstart qend sstart send length qcovhsp pident evalue stitle

[lieven.sterck]

out of curiosity: are you getting decent result when running diamond in blastx mode? When I tried it the results were horrible (but it's been a while).