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jts / nanopolish

Signal-level algorithms for MinION data
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nanopolish polya outputting NO FILE LOADED #1118

Open glf20 opened 7 months ago

glf20 commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

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

wangziyuan66 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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

glf20 commented 5 months ago

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

Thanks