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nanoporetech / pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish
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Pipeline stuck on cluster_gff for big input files #15

Closed MilesLuca closed 3 years ago

MilesLuca commented 4 years ago

Hi Botond,

This issue is related to this post on the pinfish github.

Pinfish appears to get stuck on the cluster_gff step. The cluster_memberships.tsv file reaches a maximum file size of 653089935 bytes and then stops.

The pipeline runs fine when supplying it with smaller fastq input files suggesting this may be a memory issue. However, I do not see an option to supply more memory.

The input GFF is 4.4G and I'm running with -c 5 and -t 15.

Changing thread number makes no difference, pipeline stuck at same step and same file size.

Thanks for your help,

Luca.

bsipos commented 3 years ago

This pipeline is no longer recommended for reference-based isoform analysis. Please use the newer pipeline-nanopore-ref-isoforms pipeline instead.