Hello everyone whenever i run this command this error terminates the command. can someone please guide me

Question

[mibtisamnasar]

Hello everyone whenever i run this command this error terminates the command. can someone please guide me

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

[WouterDeCoster]

Make sure that the --sequencing-summary argument points to the, well, sequencing_summary.txt file.

[mibtisamnasar]

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 sequencing_summary_FAN37212_36470888.txt nCoV-2019/V3 barcode06

usage: artic [-h] [-v] {extract,basecaller,demultiplex,minion,gather,guppyplex,filter,rampart,export,run} ... artic: error: unrecognized arguments: barcode06

[WouterDeCoster]

Was that a question?

[mibtisamnasar]

where am i wrong and what is the right one as i want to generate consensus sequence and VCF files (variant calling file)

[cpad0112]

Could not find fast5 filename column in the header of /home/mibtisamnasar/USB_Minion/minion/ARCTIC_PAK2/02/20210331_1129_MN33669_FAN37212_d1ef496e

Answer 1

[colindaven]

@mibti

What Wouter was saying was 1: This - from your command - doesn't look correct. After the 496e there is a space before the sequencing_summary file starts

--sequencing-summary /home/mibtisamnasar/USB_Minion/minion/ARCTIC_PAK2/02/20210331_1129_MN33669_FAN37212_d1ef496e sequencing_summary_FAN37212_36470888.txt

1. The error message is complaining about barcode06 at the end of your command.

I'm not sure how to solve this since I don't have the pipeline running here. Solve question 1 first though.