Comments (6)
I think it is an underflow but I thought I fixed this. Just confirming but your filtered.fastq is extremely small right?
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You are right, it should be an underflow instead of an overflow.
The FASTQ has only 3 reads.
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so as I understand the problem is there isn't enough reads to sample and every value should be 0 in that tsv aside from F1 so that is definitely a bug but what is the user's intention in using a file with only three reads?
from ntcard.
so as I understand the problem is there isn't enough reads to sample and every value should be 0 in that tsv aside from F1 so that is definitely a bug but what is the user's intention in using a file with only three reads?
It's easier/better to run an assembler on a file and see if it fails or succeeds to assemble anything rather than predict if/when it will fail or succeed.
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@jowong4
I remember you fixed this issue, right?
need to add an error exception for ntcard on too few read/kmers.
from ntcard.
We had quite a picnic with this bug, in our case it happened because ntCard uses the name of the read to determine the type of the file, not sure why this is even needed.
The offending function is: getftype @ ntcard.cpp
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Related Issues (20)
- ntcard file.gbk fails, but file.gff works? HOT 6
- K-mers with odd frequency having 0 counts HOT 9
- Support Uracil nucleotides in input files HOT 5
- Reg: kmer dump generation HOT 1
- Support for U bases not working properly HOT 2
- ntcard run error: Abort trap 6 HOT 3
- ntCard report interpretation HOT 3
- v1.2.0 does not work with FASTA files HOT 4
- Compilation blocked because of Werror HOT 1
- Jagged kmer coverage profiles with gzipped FASTA HOT 3
- Setting the verbosity arguments HOT 3
- Integer overflow on calculating kmer distribution HOT 5
- ntcard with lrz compressed files HOT 1
- MACOS problem HOT 2
- Problems w.r.t speed of ntCard and accuracy in genome size estimation HOT 8
- Use of read names to determine input file type
- Do you plan to upgrade to latest nthash
- dyld: cannot load Abort trap: 6
- Can't build from source HOT 3
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