Open alexhbnr opened 5 years ago
Yes, this is a known problem with CQF module. There is no workaround yet...
I'm having the same issue... still no solution?
I'm getting the same issue on version 3.15.2
- weird thing is it happens for one sample and not for another one... Help? @asl
Hi I think i'm having the same problem is there still no solution ?
HI.
I hope this will help in solving this problem in future releases.
Sample background: Mice faecal metagenome Sequencer: HiSeq 2500 250bp pair-end reads Number of samples: 4
QC KneadData (filtering of PhiX, mouse, and human genome)
Error-correction bfc
Assembly
SPAdes 3.15.4
command :
spades.py --meta -1 sample1_R1_bfc_corrected.fq.gz -2 sample1_R2_bfc_corrected.fq.gz -o sample1 -t 10 -m 150
Here, two of my sample were successfully assembled, and two stuck at Spades-hammer reverse read K-mer Counting.
I repeated every step from QC for these two failed samples but again, the same problem.
So I skipped bfc correction for these two samples, leading to successful assembly using the above command.
I was just wondering if you haven't performed bfc correction, and your assembly is stuck at Spades-hammer reverse read K-mer Counting, will bfc correction help?
Regards,
Bhim
When running metaspades on a paired-end FastQ files with error correction enabled,
spades-hammer
process through counting the k-mers on the forward reads, but gets stuck on doing the same on the reverse reads.While it took less than 20 minutes on the forward reads, it did not proceed through the reverse reads after more than 4 hours when I terminated the process. The process was running on full force all time using all specified CPUs but didn't proceed to the next step.
I started analysing the data on multiple different machines while specifying different amounts of max memory and number of threads, but I always end up with the same results. Other samples from the same sequencing run could be processed with issues.
Any ideas what this could be caused by and how I circumvent it?
Here is the
params.txt
:And the
spades.log
: