# Aric MinION pipeline compaible with new demultiplexing - Nanopolish with fast5 in subfolder

**URL:** <https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286>\
**Category:** Bioinformatics\
**Created:** [15 March 2021 09:26 UTC](https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286 "2021-03-15T09:26:47Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![weehzer](https://avatars.discourse-cdn.com/v4/letter/w/df788c/32.png) [@weehzer](https://community.artic.network/u/weehzer)\
**Post date:** [15 March 2021 09:26 UTC](https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286/1 "2021-03-15T09:26:48Z")

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Hi,  
the new versions of MinKNOW allows to demultiplex with the option “requiring barcodes at both ends”, which is what we need for the artic pipeline.  
However, recently not just the fastq files but also the fast5 files will be in subfolders devided by barcode.  
e.g. path\_to\_fast5/barcode01/ _.fast5; path\_to\_fast5/barcode02/_ .fast5 etc.

In the artic pipeline in the following step:

> artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer\_schemes --read-file run\_name\_barcode03.fastq --fast5-directory path\_to\_fast5 --sequencing-summary path\_to\_sequencing\_summary.txt nCoV-2019/V3 samplename

Do we have to point to the fast5 folder or e.g. fast5/barcode01 folder. Or is there some kind of -r (recursive) option?

I don’t really get how nanopolish matches the fast5 and the fastq and I am worried polishing will fail if the path is not set the right way.

Thanks!

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**Author:** ![mIbtisamnasar](https://avatars.discourse-cdn.com/v4/letter/m/9d8465/32.png) [@mIbtisamnasar](https://community.artic.network/u/mIbtisamnasar)\
**Post date:** [5 May 2021 11:44 UTC](https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286/2 "2021-05-05T11:44:36Z")

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Hi, i am facing issue with artic pipeline if someone can help me it would be great as the error i am facing is mentioned below

_artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer\_schemes --read-file run\_name\_barcode06.fastq --fast5-directory /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e/fast5\_pass/barcode06 --sequencing-summary /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e nCoV-2019/V3 barcode06_

> Running: nanopolish index -s /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e -d /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e/fast5\_pass/barcode06 run\_name\_barcode06.fastq

**Could not find fast5 filename column in the header of /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e**

> Command failed:nanopolish index -s /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e -d /home/mibtisamnasar/USB\_Minion/minion/ARCTIC\_PAK2/02/20210331\_1129\_MN33669\_FAN37212\_d1ef496e/fast5\_pass/barcode06 run\_name\_barcode06.fastq