terminate called after throwing an instance of 'std::bad_array_new_length'

[ufaroooq]

Hi, I was trying to run Fastplong on some Nanopore long reads generated from R10.4 cell.

the command I used is
fastplong --in=NP_fastq/NP01_porechoped.fastq.gz --out=NP_fastq/NP01_fastplong.fastq.gz --compression=4 --disable_adapter_trimming --qualified_quality_phred=10 --length_required=2000 --json=NP_fastq/NP01_report.json --html=NP_fastq/NP01_report.html --report_title=NP01_fastPlong_report --thread=16 --verbose

and i get the following error in log file
Filtering result: reads passed filter: 0 reads failed due to low quality: 0 reads failed due to too many N: 0 reads failed due to too short: 0 terminate called after throwing an instance of 'std::bad_array_new_length' what(): std::bad_array_new_length /vast/ti78qem/scripts/0.scripts/seqdata_qc/run_fastplong.sh: line 44: 4151269 Aborted (core dumped)

I have attached the complete Log file too.

Can you help with this.
NP01_fastPlong.log

[mbacino]

I am dealing with the same issue with my Nanopore long reads generated from a R10.4.1 flow cell:

fastplong.0.2.0 --in "$INPUT_FASTQ" \
    --out "$FASTPLONG_OUTPUT" \
    -A \
    -l 200 \
    -q 20 \

Before filtering:
total reads: 3715434
total bases: 4246639024
Q20 bases: 3882583993(91.4272%)
Q30 bases: 3595978081(84.6782%)

After filtering:
total reads: 0
total bases: 0
Q20 bases: 0(-nan%)
Q30 bases: 0(-nan%)

Filtering result:
reads passed filter: 0
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
terminate called after throwing an instance of 'std::bad_array_new_length'

[mbacino]

It isn't a solution, more like a work around, but I have had success with filtlong
https://github.com/rrwick/Filtlong

[sfchen]

This should be caused by some bug, can you kindly upload some data that I can reproduce this issue?

And surely I will fix it soon.