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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Error in artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file run_name_barcode06.fastq --fast5-directory #72

Open mibtisamnasar opened 3 years ago

mibtisamnasar commented 3 years ago

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

Screenshot from 2021-05-28 21-23-13

FairerBadge66 commented 2 years ago

Add the sequencing summary filename at the end of the corresponding path:

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