spades; Failed to align paired reads
I ran spades with this command line
./spades.py -k 21,33,55,77,99,127 --careful --only-assembler -1 11-0910_S7_L001_R1_001.fastq.gz -2 11-0910_S7_L001_R2_001.fastq.gz -o 11_0911
and at the end
=======
SPAdes pipeline finished WITH WARNINGS!
===
Error correction and assembling warnings:
* 0:00:04.945 4M / 8M WARN General (dataset_processor.cpp : 256) Failed to align paired reads /Users/apple/Desktop/SPAdes-3.6.2-Darwin/bin/11-0910_S7_L001_R1_001.fastq.gz and /Users/apple/Desktop/SPAdes-3.6.2-Darwin/bin/11-0910_S7_L001_R2_001.fastq.gz
What should I do next ?
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Spades has finished with a warning, but not with an error. Please inspect the content of the output directory ./11_0911 carefully. You will find there a log file and the contigs.
I also have the same issue... Also I checked the output directory and there is not contigs or scaffolds in it.
I checked also my input data and is OK... the kmer used were -k 15,21,33,55,67,79,91
As soon as I leave default parameters or reduced the last 91 kmer the error disappeared. I don't know exactly why this happened but, it seems to works now.
Cheers.
Spades warns you, that the coverage with K91 is too low. Note that coverage decreases with increasing kmer size. Do not run with large kmers if you do not have enough coverage.