Description
Hello, thank you for developing such an excellent tool for third-generation transcriptome analysis. I am currently using it to process ONT data from cattle. Everything in my processing script runs perfectly, but as shown in the image, the polya_results.tsv file generated at the end has READ_FAILED_LOAD for all qc_tag entries. I'm not sure what went wrong. I’ve seen similar issues mentioned on the forum, but none of them seem to have a definitive solution. Could you please let me know how to resolve this error?
Many thanks and best wishes.
[### 1. build index
singularity exec ${singularity_path}/nanopolish:0.14.0--hee927d3_5 nanopolish index --directory=${fast5_dir} ${fq_file}
2. align and sort
singularity exec ${singularity_path}/minimap2:2.28--he4a0461_0 minimap2 -t ${threads} -ax splice -ub -k14
${genome_fasta} ${fq_file} > ${sample}.sam
singularity exec ${singularity_path}/samtools:1.9--h91753b0_8 samtools
view -hSb ${sample}.sam |
singularity exec ${singularity_path}/samtools:1.9--h91753b0_8 samtools
view -q 10 -F 2304 -hb - |
singularity exec ${singularity_path}/samtools:1.9--h91753b0_8 samtools
sort -o ${sample}.sorted.bam -
3. identify ployA
singularity exec ${singularity_path}/nanopolish:0.14.0--hee927d3_5 nanopolish
polya --threads=${nthreads} --reads=${fq_file} --bam=${sample}.sorted.bam --genome=${genome_fasta} > ${sample}_polya_results.tsv](url)