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Hello everyone,
I use nanopolish to prepare my data for the next steps of my pipeline, and to have an estimation of polyA tail size:
nanopolish index -d $fast5 $fastq
nanopolish eventalign --reads $fastq --bam $bam --genome $genome --scale-events --signal-index --summary $sample_summary --threads $task.cpus > $sample_eventalign
nanopolish polya --reads $fastq --bam $bam --genome $genome --threads $task.cpus > $sample_polya
But I have this error:
[readdb] indexing fast5
[readdb] num reads: 25957033, num reads with path to fast5: 25718969
[E::bgzf_read_block] Failed to read uncompressed data at offset 4850678: Stale file handle
[E::fai_retrieve] Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?)
[E::fai_retrieve] Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?)
terminate called recursively
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string: construction from null is not valid
.command.sh: line 3: 247145 Aborted nanopolish eventalign --reads WT6_sup_RNA_seq_output_align_tail.fastq.gz --bam WT_R1.sorted.bam --genome Mus_musculus.GRCm38.dna.primary_assembly.fa --scale-events --signal-index --summary WT_R1_summary.txt --threads 32 > WT_R1_eventalign.txt
The step of eventalign seem to not working. Is it because there not enough memory and I must segmented the bam per chromosome ?
The Flowcell used is FLO-PRO004RA, I don't think I need to use f5c.
Can you help me?
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