Using nanopolish polyA with f5c index error

[kir1to455]

Hi,
I have encountered the same problem as below.
#125
I created readdb using the following code.
echo -e "*\t/public3/hjliang/SARS_CoV_2/slow5/CoV2_A549_1/CoV2_A549_1.blow5" > /public3/hjliang/SARS_CoV_2/fastq_file/CoV2_A549_1_chrSCV.fastq.index.readdb

And my nanopolish polya code:
nanopolish polya --reads CoV2_A549_1_chrSCV.fastq --bam ${subset_bam_dir}/${bbase}.SARS.${orfname}.sorted.bam --genome ${index_dir}/SARS-CoV-2.fa --threads 40 > ${PolyA_dir}/${bbase}.${orfname}.poly.tsv

I got the result show all is -1.0 and the last column are all READ_FAILED_LOAD.
My nanopolish version is 0.14.0.
Did I make a mistake somewhere?

Best wishes,
Kirito

[hasindu2008]

Is this R9.4 data or latest R10.4 data? And is it CDNA or direct-RNA?

[kir1to455]

Direct RNA-sequencing data with R9.4.1

[hasindu2008]

I think I know the issue, there was a bug that affected the SLOW5 with polyA which was fixed a bit later after the v0.14.0 here. Would you be able to try compiling nanopolish latest commit from the master branch?

[kir1to455]

Hi, I have compiling nanopolish latest commit and it shows the correct results.
Thanks for your help!

Best wishes,
Kirito