Error in split_libraries_fastq.py: No filepaths match pattern/name '--sample_ids'.

[francesca de martini]

Hello, 

I run my 18S samples using 2X300bp Miseq. The facility sent me back the data already demultiplexed in different r1 and r2 files one for each sample. I used pandaseq to merge the r1 and r2 files together for each sample.  The output from pandaseq is a merged fastaq file for each sample. Since then I have been trying to use this command to label my sequences and combined them all together:

multiple_split_libraries_fastq.py -i split_library_input/ -o test --demultiplexing_method sampleid_by_file --read_indicator .paired -p /Users/francescademartini/Desktop/Methods/NEXT_GEN/scrpts_pipelines/parameters\ files/multiplesplit.txt --sampleid_indicator .

But it gives me this error:

*** ERROR RAISED DURING STEP: split_libraries_fastq.py

Command run was:

 split_libraries_fastq.py --phred_quality_threshold 19 --sample_ids 158.,159.,162.,163.,164.,165.,166.,167.,168.,169.,170.,172.,173.,175.,176.,177.,178.,179.,180.,181.,182.,183.,184.,185.,186.,187.,188.,189.,190.,191.,192.,193.,194.,195.,196.,197.,198.,199.,200.,201.,202.,203.,204.,205.,206.,207.,208.,209.,210.,211.,212.,213.,214.,215.,216.,217.,218.,219.,220.,221.,222.,223.,224.,225.,226.,227.,228.,229. --phred_offset 33 -i  --sample_ids  -o /Users/francescademartini/Desktop/Projects/Illumina_library_prep/Illumina_run_July_17/DATA/saperate_projects/Heterotermes_sp/test  --barcode_type 'not-barcoded'

Command returned exit status: 2

Stdout:

Stderr

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

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I don't understand what I am doing wrong. Attached you find my parameter file, my mapping file and also a couple of examples for the merge files. 

Thank you so much for your help!

Francesca