Open mbiokyle29 opened 2 years ago
Hi mbiokyle29, Did you resolve this issue? I have the same problem with the function query.
The jellysish count works fine :
jellyfish count -m 40 -s 100M -t 23 -C myfile.fastq -o mer_counts_40.jf
but then I got that when using query :
jellyfish query mer_counts_40.jf CTCACTCGCTCAGCTATAAGAAGAGCCTCAACCATTGAAA
[E::hts_open_format] Failed to open file "" : No such file or directory
libc++abi: terminating due to uncaught exception of type std::runtime_error: Can't open SAM file ''
zsh: abort jellyfish query mer_counts_40.jf CTCACTCGCTCAGCTATAAGAAGAGCCTCAACCATTGAAA
Can someone guess what's happening?
Thanks,
MA
@MAfustier I was never able to find a resolution for this. I opted for making a dump of the database in columm format and loading into memory as needed. I dont recall the exact command, but I think it was trivial (jellyfish dump -c
or something)
I am having the same issue with the query function.
The error I get when running a query is as follows:
libc++abi: terminating due to uncaught exception of type std::runtime_error: Can't open SAM file '' zsh: abort jellyfish query UViGs.jf AACGTTG
Wondering if this is an issue specific to Mac software?
I am experiencing the following issue with the
query
command. I've build a kmer database from hg38 using the following command:jellyfish count -m 15 -t 5 -s 100M -L 5 -o hg38.15.jf hg38.fa
My goal was to build a 15mer database, keeping only kmers with at least 5 hits. This command completes, and I get a database file like so:
With the database in hand, I went to
query
, like so:jellyfish query hg38.15.jf AACCTGGGAGGAGGA
But I get an error like:
Oddly, if I re-run the command several times, The contents in the "" change, ex:
I am on the following version:
installed via homebrew
I also tried building from source, and get a slightly different error