ckennedy-nmdp
commented
9 years ago It does work with an unpaired FASTQ files from the SRA.
L0500503:pipeline int33484$ SSAKE -f ~/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq -w 1 -h 1 -m 50 -o 30 -c 1 -e 0.90 -k 4 -a 0.1 -x 20
Running: /usr/bin/SSAKE [v3.8.1] -f /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq -s no-s -i 0 -h 1 -w 1 -m 50 -o 30 -r 0.7 -t 0 -c 1 Coverage: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.coverage.csv Read position: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.readposition -z 100
Contigs: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.contigs Singlets: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.singlets
Excluded reads: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.short Log: /Users/int33484/Documents/Projects/Hackathon/work/pipeline/raw/DRR003809.fastq.ssake_m50_o30_r0.7_t0_w1_pid94926.log
=>Reading sequences initiated Wed Oct 22 18:24:00 MDT 2014 Sequence reads loaded: 145689 total sequences (130928 unique) Number of unique seed sequences: 130928
=>Sequence assembly initiated Wed Oct 22 18:24:14 MDT 2014 +---------1---------2---------3---------4---------5---------6---------7---------8---------9---------+ x 10 [% complete] ..................................................................................................... Contig assembly executed normally Wed Oct 22 18:33:51 MDT 2014
ghost
https://github.com/nmdp-bioinformatics/pipeline/blob/master/process_fastq.bash#L136
is passing though unpaired FASTQ formatted sequences into SSAKE using the -f option, which will not work.