Qiime 1.9.1: split library: illumina paired end: error No filepaths match

[Sanjeev Sariya]

Hi Team,

I'm having 256 bp read length, V3V4 Illumina reads. V3V4 region. 

Data produced by Dual index approach - Fadrosh et al. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

I know QIIME doesn't provide support for this data. 

I'm receiving an error at split library step.

I'm following instructions from:

https://groups.google.com/forum/#!topic/qiime-forum/8r_FAM9l7oI

Bar code length 12.

Qiime version: 1.9.1

Step I followed:

1) Join the reads:

Tool used: fastq-join - Version: 1.01.759 ea-utils

join_paired_ends.py -f APJR2_R1.fastq.gz -r APJR2_R2.fastq.gz -o ./  -j 30

3 files: joined, unjoined- Read1 and unjoined Read2

2) Extract barcode:

Bar code length 12

extract_barcodes.py -f fastqjoin.join.fastq -c barcode_paired_stitched --bc1_len 12 --bc2_len 12

Get output: barcodes and reads.fastq 

3) Use the barcodes file in split_library

[sariyasanjeev@login3 30]$ split_libraries.py -i ./fastqjoin.join.fastq -o ./ -b barcodes.fastq -q 20 

------------------------------------------------------------

Error:

Error in split_libraries.py: No filepaths match pattern/name '20'. All patterns must be matched at least once. 

--------------------------------------------------

I'm working in the directory where files are present. Only 20 I can see is quality one in parameters. No other files with 20 are present in working directory

As far as I've worked with Qiime 1.9.1, it doesn't need (or needed )mapping file.

Any help shall be highly appreciated.

Thanks,

Sanjeev

[Daniel McDonald]

Hi Sanjeev,

I've opened a discussion internally on this and we'll get back to you soon.

Best,

Daniel

[TonyWalters]

Hello Sanjeev,

I think you chose the older split_libraries (for 454/iontorrent data) in this command:

split_libraries.py -i ./fastqjoin.join.fastq -o ./ -b barcodes.fastq -q 20 

Can you try this instead:

split_libraries_fastq.py -i ./fastqjoin.join.fastq -o ./ -b barcodes.fastq -q 20 

You might also choose a different output directory rather than writing to the current directory-mostly just for organizing your data and preventing files from being overwritten later, it shouldn't be responsible for the issue you're seeing now.

[Sanjeev Sariya]

Hi Tony and Daniel,

Thanks much for your reply.

Script worked with 

split_libraries_fastq.py

Its embarrassing, clearly I missed trees for the forests. :)

Appreciate your help.