IndexError: list index out of range

[Enorya]

Hello,

I'm trying to use the demultiplex script of miniBarcoder on a dataset but I got the following error:

Traceback (most recent call last):
  File "miniBarcoder/mb_parallel_demultiplex.py", line 571, in <module>
    parts=partlist1[lens[-1]:]
IndexError: list index out of range

Before this I have the following lines:

13
6 660 660
666 29599 28933
Non-interleaved file generated
polar-cod_L1400-1750.fasta_reformat_out_1pdt_p polar-cod_L1400-1750.fasta_reformat_out_2pdt_p

and my command look like this:

miniBarcoder/mb_parallel_demultiplex.py -d demfile_comp16S.txt -l 1400 -o miniBarcoder_results/demultiplexed_comp16S/ -f cleaned_separated/polar-cod_L1400-1750.fasta

Do you have any idea why I have this issue?

Thank you in advance for your help,
Enora

[asrivathsan]

Hello,

Sorry for the delay, I had been on leave. If the issue has persisted, would it possible to share the file sizes of the output folder. Else a sample file to help understand?

Thanks
Amrita

[Enorya]

Hello,

Yes the issue still persist. This is what the output directory looks like:

drwxr-x--- 2 vsc34088 vsc34088      8192 Mar 23 11:56 demultiplexed
-rw-r----- 1 vsc34088 vsc34088 508525175 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out
-rw-r----- 1 vsc34088 vsc34088         0 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_1pdt
-rw-r----- 1 vsc34088 vsc34088 508525175 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt
-rw-r----- 1 vsc34088 vsc34088  30876495 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_paa
-rw-r----- 1 vsc34088 vsc34088  30885590 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pab
-rw-r----- 1 vsc34088 vsc34088  30928461 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pac
-rw-r----- 1 vsc34088 vsc34088  30984909 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pad
-rw-r----- 1 vsc34088 vsc34088  31044055 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pae
-rw-r----- 1 vsc34088 vsc34088  30853728 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_paf
-rw-r----- 1 vsc34088 vsc34088  30906858 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pag
-rw-r----- 1 vsc34088 vsc34088  30627328 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pah
-rw-r----- 1 vsc34088 vsc34088  30661803 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pai
-rw-r----- 1 vsc34088 vsc34088  30693577 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_paj
-rw-r----- 1 vsc34088 vsc34088  30765196 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pak
-rw-r----- 1 vsc34088 vsc34088  30810683 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pal
-rw-r----- 1 vsc34088 vsc34088  30865856 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pam
-rw-r----- 1 vsc34088 vsc34088  30900824 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pan
-rw-r----- 1 vsc34088 vsc34088  30936728 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pao
-rw-r----- 1 vsc34088 vsc34088  30906360 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_pap
-rw-r----- 1 vsc34088 vsc34088  14876724 Mar 23 11:57 polar-cod_L1400-1750.fasta_reformat_out_2pdt_paq
-rw-r----- 1 vsc34088 vsc34088    503183 Mar 23 11:57 temp1.fas

The demultiplexed/ folder is empty.
I sent you with WeTransfer a compressed version of my fasta file so that you can test it yourself.

Enora

[asrivathsan]

Dear Enora,

Thanks, I have obtained the file, if you could also share with me the demultiplexing file i can then proceed

best wishes
Amrita

[Enorya]

Oh sorry, I forgot to put the demultiplexing file, here it is:
demfile_comp16S.txt

Thank you for your help on this!

[asrivathsan]

Hi Enora,

I think you have to include splitlength option by specifying -s
Essentially I think it would work if you do:

miniBarcoder/mb_parallel_demultiplex.py -d demfile_comp16S.txt -l 1400 -o miniBarcoder_results/demultiplexed_comp16S/ -f cleaned_separated/polar-cod_L1400-1750.fasta -s 1400

This option splits your sequences into specific length chunks to identify ligated products. It is defaulted to 650. This means it considers everything under 6502 as a single product (i.e, 1300 bp). While in your case, it can be set at 14002

[Enorya]

Hi,

Sorry for the delay I didn't had much time during the last 2 weeks to try your solution.
I just tested it and your solution worked!
I just have some questions about the results. I tried 2 different datasets and I don't have the same outputs for both.
For the first one (the one I sent you) I have the demultiplexed/ folder and 6 other files: dmpfile, dmpfile_tagfr, ...reformat_out, ...reformat_out_1pdt, ...reformat_out_2pdt and temp1.fas
For the second dataset I have the same files and 4 more: ...reformat_out_2pdt_paa, ...reformat_out_2pdt_pab, ...reformat_out_2pdt_pac, ...reformat_out_2pdt_pad
Can you explain me what are the different outputs? Is the number of outputs linked with the number of ambiguous bases in the primers (because in the second dataset the primers are CCTACGGGNGGCWGCAG and GACTACHVGGGTATCTAATCC)?

Also, I was wondering if your tool trim the tags and primers from the reads? It seems I'm not able to find them in the reads after the demultiplexing but I want to be sure.

Thank you for your help!