Yesterday, the run was cancelled due to an error with writing unitigs1 in the abyss-run:
abyss-pe k=48 se="SRR1817238.fastq" name=p-andina-assembly-untrimmed "unitigs1"
I also experienced a problem with not having enough space on my home directory, where I had exceeded the quota of 32 Gb and had data of ~38 Gb. This is because the FASTQ-file with raw sequencing data is 16Gb, and the trimmed version of data (using sickle) is 14Gb. I therefore downloaded the trimmed version locally to my computer for now, until the assembly of the original FASTQ-file is working. When it is working, the trimmed version will be uploaded and run with ABySS.
A new job was submitted (10 hours run) where the unitigs1 part was removed:
#!/bin/sh
cd /home/ellinor/Project
# modules needed
module add bioinfo-tools
# module add python
module add abyss/2.0.2-k128
# Assembly using ABySS
# se="" takes only single-reads as input, even though we run the abyss-pe mode
abyss-pe k=48 se="SRR1817238.fastq" name=p-andina-assembly-untrimmed
And from what I can see today it seems to have worked, but I only base this on the fact that I have the expected output-files in the directory. However we are missing a .contig- and a .scaffold-file which another group got that used ABySS but in that case they had paired-end reads, and this does not have to mean the assembly did not work. When looking at the .out-file, no error messages are found. The statistics from the assembly can be seen below.
$ cat p-andina-assembly-untrimmed-unitigs.fa
n n:500 L50 min N80 N50 N20 E-size max sum name
2840597 43385 13871 500 616 897 1525 1133 5973 38.34e6 p-andina-assembly-untrimmed-unitigs.fa
The quality of the assembly will be assessed the next coming days by running several different k-mers, and also use the trimmed sequences obtained using sickle. But as it seems now, no scaffolding has been performed (even though we have read that ABySS has an in-built scaffolding tool), and this means we will have to look into different scaffolding tools. But that’s for Monday.