opengene/defq

Please switch to https://github.com/OpenGene/defastq

defq's Issues

What is the difference between defq and defastq software

I downloaded the defastq software through this link：
http://opengene.org/defastq/defastq

What is the difference between defq and defastq software?

Enhancement Memory Control

When I extract the fq.gz from size 30G data(fq.gz), the memory will be large, was killed by the system.

defq.sh: line 2: 95033 Killed /Bioinfo/tools/defq --in1 Undetermined_S0_R1_001.fastq.gz -s /Task/OUT/index2.sheet -o /Task/OUT/P5index -f _R1.fastq.gz

15024 fastq 20 0 70.4g 70g 1420 S 2368.2 55.7 456:49.89 defq

deadlock may happen when writing is too slow

cannot demultiplex

Hi, I don't understand what is wrong ...

I have a fastq file with the following sequences. (My barcode is under bracket):

@MN00591:192:000H332YK:1:11102:20930:2477 1:N:0:1
GCCCCCAAAATCAGCGAAATGGGCGCCATTGGTGATGACACCAGGCATCAGAATAAATGTTGTCGGCGAGATATTTGTCGGTCCCAGACTTTCGCTGAACGGCCACGGAGATAGGGCTAGGAGTAACCAGAATGGAGAACGC  [ATATCATTAACAGAG]  GGTACGCTCATCAGAATTAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

My barcode file contains the barcode :

#filename,#index1,#index2
A11,ATATCATTAACAGAG,  
H10,ATTAATAGTGGTATG,

But the following command keep creating 0 bytes files.

defq -i file.fastq -o demux_out_dir -s index.csv -f .fastq -z 1