how to demultiplex unknown casava version fastq file ?

[mariabernard]

Dear all,

I am trying to use iu-demultiplex to work with those fastq files : https://github.com/caporaso-lab/mockrobiota/blob/master/data/mock-9/dataset-metadata.tsv

but it's seems to no be FASTQ file generated by CASAVA 1.8, as iu-demultiplex return me this error :

          Header lines in your FASTQ file does not seem to be the ones illumina-utils     
          expects to see in a FASTQ file generated by CASAVA 1.8. If you call this        
          funciton with 'raw = True' parameter, all should be fine. If you are accessing  
          this function through a client, or in other words if you have no idea what this 
          message is telling you, try to re-run the program with --ignore-deflines        
          parameter. If that parameter is not available to you, then please send an e-mail
          to [email protected]

and I don't undertstand " 'raw = True' parameter ", as it's not an option of iu-demultiplex. Could you tell me if it's possible to use your program with those data ?

They looks like this

head mock-forward-read.fastq

@ILLUMINA_0331:1:1101:1214:2235#NNNNNNNNNNNN/1
TACGTAGGGCGCAAGCGTTGTCCGGAATTANTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
a_aeceeegggggiiiiiiighiiihehifBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

head mock-index-read.fastq

@ILLUMINA_0331:1:1101:1214:2235#NNNNNNNNNNNN/1
NNNNNNNNNNNN
+
YYYYYYYYYYYY

head mock-reverse-read.fastq

@ILLUMINA_0331:1:1101:1214:2235#NNNNNNNNNNNN/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

(its not always NNNNNNN in the index file)

Kind regards

Maria

[meren]

Maria, the error message says use --ignore-deflines if none of this makes any sense. Did you try doing that?

[mariabernard]

I could not find this option in the program help section.

I tried

iu-demultiplex --ignore-deflines -s sample_barcode.txt --r1 mock-forward-read.fastq.gz --r2 mock-reverse-read.fastq.gz --index mock-index-read.fastq -o output/

and I received this error

iu-demultiplex: error: unrecognized arguments: --ignore-deflines