Open MikeEHMatson opened 6 years ago
Hi Mike,
Can you please try '-B 0' in the de novo approach?
Cheers, Andy
Hi Andy, That didn't seem to change anything, and the "sortBNX failed" message still appears.
Mike
Hi Andy, I'm still having the issue and was wondering if there were any other things I might be able to try.
Thanks, Mike
Hi Mike,
Sorry for the delayed reply.
Did you get your bnx file from the Irys platform or the saphyr platform? I only tested the bnx files from the Irys platform and they worked well.
Did you try different parameters, such as the min molecule length? Looking through, it seems you used 50Kb and perhaps you have filtered many maps.
Cheers, Andy
Hi Andy, I tried reducing the molecule length cutoff to 10kb, without success. I also tried eliminating the minimum memory requirements, and reducing the number of CPUs and jobs, both of which didn't seem to change anything. I also removed the "-B" option from the command, which appears to not be relevant to runBNG denovo anyway, though this also did not fix the error.
The bnx files are from an irys, and not a saphyr platform.
Mike
Hi Mike, In the bnx sort step, the key parameters are: -l, -m and -B. Can you please check the stats of your bnx file and adjust ' -l ' in the denovo step? May try 150 or 100. Cheers, Andy
Hi Andy, i have tried several different combinations of varying -l, -m, and -B, but they all still result in the same error. I am starting to suspect the input bnx file is to blame, as it was supplied as a single already-merged .bnx file.
While the mqr step has worked previously on this already-merged file (the denovo step is using that output, though using the original .bnx file still gives the sortBNX error), I ended up not filtering the original file because I got a similarly frustrating error when running
runBNG bnxfilter -b $bnx -t 16 -m 45 -r $refAligner -o filter -p filter_04
which gave
Opps! Your input '' is not an integer or smaller than 0. Please check!
Not sure what input I am missing there.
Mike
Hi Mike,
I found in the bnxfilter function, I made a typo error on Line 888. "minLen" should be "minlen" (runBNG has been updated). This error has no association with the denovo function. Not sure why it cannot be applied to your bnx file since you have already tried different settings.
You may try 'bnxmerge' to reorganise your bnx file with only one input. If the problem is still there, I'm afraid I cannot give a further help.
Cheers, Andy
Hi Mike,
Can you please try '-B 0' in the de novo approach?
Cheers, Andy
Excuse me, I wonder what the "-B" (maximum backbone intensity) parameter mean. Could you please tell me? Thanks a lot!
Best, Joy
Hi @MikeEHMatson ,
I want to ask how you solved this problem before? I keep reporting this problem when I run it, and it has not been resolved. I hope to get your reply. Thanks
Hello, I think I am having a similar issue to the one described last year by GWheelerEB.
Trying to run command:
runBNG denovo -b mqr/MQR_table_rescaled.bnx -t $tools -s $scripts -T 16 -S 45 -j 16 -l 50 -z 50 -r $refCMAP -p 0.95 -n 0.09 -d -0.03 -f 0.22 -R 0.03 -o denovo
But getting:Changing around some of the CPU or memory settings doesnt help, nor switching the input .bnx files (which are outputs of runBNG mqr) to the original, nonmodified, .bnx files changes the error.
Currently running the most recent release (1.03-cda06f4).
Thanks, Mike