nanopolish polya outputting NO FILE LOADED

[glf20]

Hi,
Whenever i run a nanopolish polya run with my dRNA dataset i get an empty file with each read saying 'NO FILE LOADED'. Commands and output as below:

Command: nanopolish index -d /20230927_1043_MN38033_FAX31978_99230b36/fast5_pass/ -s ./sequencing_summary.txt ./pass/polya.fastq

Output: [readdb] indexing /mnt/lustre/RDS-20230927_1043_MN38033_FAX31978_99230b36/fast5_pass/
[readdb] num reads: 1252505, num reads with path to fast5: 1252505

Command: minimap2 -a -x map-ont ../OM830318.fasta polya.fastq > polya.sam

Command: nanopolish polya --verbose --reads polya.fastq --bam polya.sorted.bam --genome ../OM830318.fa > polya_results.tsv

Output: [post-run summary] total reads: 601580, unparseable: 0, qc fail: 0, could not calibrate: 0, no alignment: 0, bad fast5: 300790

[jts]

Hi,

Are you using the latest nanopolish? The final log message suggests you're using an older version as there was a double-counting bug in some old versions.

Jared

[wangziyuan66]

I have that problem too. I am currently using v0.14.0

[wangziyuan66]

Oh by the way, for my problem after I run nanopolish polya I will get the output but most of my reads have qc tag READ_FAILED_LOAD, some of the reads are PASS but the proportion of READ_FAILED_LOAD is very large maybe 90%.

[glf20]

Hi JTS,
Thanks for the reply - my version is
Guppy Basecalling Software, (C) Oxford Nanopore Technologies plc. Version 6.3.7+532d626, minimap2 version 2.22-r1101 and my version of nanopolish is
nanopolish version 0.13.2

[glf20]

see attached the output file from the polya command
polya_results.zip

[glf20]

Hi Wangziyuan66,
Were you able to work this issue out and rectify?

Thanks