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SOAPdenovo and FASTA files - Newbie question
I'm a newbie when it comes to NGS bioinformatics. I'm testing SOAPdenovo with a small FASTA file (3300 kb). The FASTA file is an unpaired set of exported reads viewed in Tablet but originally generated in a BWA alignment, i.e. I extracted a subset of reads from my MiSeq run based on a reference sequence for denovo assembly in SOAPdenovo. For an unknown reason SOAPdenovo fails to read the FASTA file. (see below)
Has anyone else seen this and is there a fix out there?
Version 2.04: released on July 13th, 2012
Compile Apr 25 2013 16:59:53
********************
Pregraph
********************
Parameters: pregraph -s soap-fasta.config -K 63 -R -o fastatest
In soap-fasta.config, 1 lib(s), maximum read length 260, maximum name length 256.
8 thread(s) initialized.
Import reads from file:
/home/fasta/1700-sorted-bam_140k.txt
--- 100000000th reads.
--- 200000000th reads.
...and on and on to "kill -9"
Has anyone else seen this and is there a fix out there?
Version 2.04: released on July 13th, 2012
Compile Apr 25 2013 16:59:53
********************
Pregraph
********************
Parameters: pregraph -s soap-fasta.config -K 63 -R -o fastatest
In soap-fasta.config, 1 lib(s), maximum read length 260, maximum name length 256.
8 thread(s) initialized.
Import reads from file:
/home/fasta/1700-sorted-bam_140k.txt
--- 100000000th reads.
--- 200000000th reads.
...and on and on to "kill -9"