Extracting reads from fastq files with BBMAP?

Question

[simplitia]

Hi I have a file with list of read ids I would like to extract from a pair-end read. This file only contains 1000 reads. When i use bbmap to accomplish this with the following command however, the resulting size of the fastq files are very similar to original and so are

/bbmap/filterbyname.sh in1=${fq1} in2=${fq2} out1=strip2_R1.fq.gz out2=strip2_R2.fq.gz names=names2.txt

This should only have 1000 reads in the new files but its in the millions!

Is there something I'm doing incorrectly? thanks!

[GenoMax]

What does names2.txt look like (show us output of head -5 names2.txt)? Remember to remove @ or > identifiers from read names in names2.txt. One read name per line in file.

[simplitia]

Hi, ok here is how the first few lines look like.

NAME1
K00153:706:H3VMJBBXY:4:1101:12601:1279
K00153:706:H3VMJBBXY:4:1101:25875:1279
K00153:706:H3VMJBBXY:4:1101:17563:1297
K00153:706:H3VMJBBXY:4:1101:18355:1297
K00153:706:H3VMJBBXY:4:1101:28178:1297
K00153:706:H3VMJBBXY:4:1101:8501:1314
K00153:706:H3VMJBBXY:4:1101:11180:1314
K00153:706:H3VMJBBXY:4:1101:22262:1314
K00153:706:H3VMJBBXY:4:1101:22648:1314

[GenoMax]

You may need to add substring=t. These should work.