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Error: denovo workflow: ``'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >`` #7

Open Malabady opened 2 years ago

Malabady commented 2 years ago

Hi,

When running the denovo workflow we get the following error:

terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >' .command.sh: line 19: 21749 Aborted (core dumped) isONclust2 sort $init_cls_options -v -o sorted Spu_full_length_reads.fq

We tried with both local and Conda environments and got the same error. Here is an example of the commands that I used:

OUTPUT=./output3 nextflow run epi2me-labs/wf-isoforms --threads 12 --fastq ./allONT-RNA_PassedReads.fastq \ --denovo --ref_genome ./genome.fasta -profile conda --out_dir ${OUTPUT} -w ${OUTPUT}/workspace --sample Spu -resume We have been dealing with this error for the last three - four days. Our HPLC people couldn't figure out the issue after trying multiple times.

Any suggestions?

Many thanks

nrhorner commented 2 years ago

Hi,

I've not come across this before. There's a thread here that might help: https://github.com/nanoporetech/isONclust2/issues/4