I'm running a abyss-pe job using trimmed paired-end MiSeq data of sample with appr. genome size of 120Mb. I trimmed my data using Trimmomatic, which gives 4 output files from the 2 original input files: 2 files are paired sequences (forward and reverse) and 2 files are unpaired sequences (forward and reverse).
I've been having problems with assembling the 4 files, it seems that abyss keeps reading the files endlessly without finishing.
The code I use is:
abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output lib='lib1' lib1='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz' se='/path/to/forward_unpaired_trimmed.fastq.gz /path/to/reverse_unpaired_trimmed.fastq.gz'
I've also tried the following with the same result:
abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output in='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz' se='/path/to/forward_unpaired_trimmed.fastq.gz /path/to/reverse_unpaired_trimmed.fastq.gz'
However, when I run the analysis with out the 'se' command it finishes reading the reads in appr. 30 min.:
abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output in='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz'
Any idea why abyss has problems reading in the files when I add the 'se' command?
Please let me know if more information is needed.
EDIT: I'm using the latest abyss version 1.9.0
EDIT 2: abyss-pe has now been running for 1250 mins, and still reading in the files, I have -v=vv on, screen shot of the verbose shows this: