Would you please be able to take a look?
I am trying to assemble a fungal genome (40Mbp size) using abyss-pe at k=96. As recommended, after importing MiSeq DNA reads, first I concatanated two sets of reads, then trimmed using BWA style trimming at q=30, then used Spades read error correction tool after which finally I did the following: 1. abyss-mergepairs (error corrected Spades reads) to obtain reads that are overlapping 2. konnector (leftover abyss-mergepairs paired reads 1 and 2) to obtain reads that are non-overlapping 3. abyss-pe with paired-end leftovers from konnector, se reads from abyss-mergepais (overlapping reads) and se reads from konnector (non-overlapping reads) with using a long function to help with the scaffold
So this is the code:
cat fungusA_read1.fastq fungusB_read1.fastq > conc_read1.fastq cat fungusA_read2.fastq fungusB_read2.fastq > conc_read2.fastq trimBWAstyle -q30 conc_read1.fastq > trim_conc_read1.fastq trimBWAstyle -q30 conc_read2.fastq > trim_conc_read2.fastq spades --only-error-correction --careful -o spades_out -t 40 -k 96 \ -1 trim_conc_read1.fastq -2 trim_conc_read2.fastq abyss-mergepairs -q30 spades_out/corrected/trim_conc_read1.00.0_0.cor.fastq \ spades_out/corrected/trim_conc_read2.00.0_0.cor.fastq konnector -j 40 -k 96 -o kon96 out_reads1.fastq out_reads2.fastq abyss-pe j=40 k=96 name=fungus lib='pe1 pe2' long='longa' \ pe1='../kon96_reads_1.fq' pe2='../kon96_reads_2.fq' \ se='../out_merged.fastq ../kon96_merged.fa' \ longa='../ref_genome.fa'
The problem is that abyss-pe hangs up after unitigs formation in the abyss-pe (last step). This is the last step nohup message:
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Mateless 667892 100%
abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match.
pe1-3.hist': No such file or directory
make: *** [pe1-3.dist] Error 1
make: *** Deleting filepe1-3.dist'