strange error with query

[Kyle McChesney]

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:

>>= stat hg38.15.jf 
16777221 40857871 -rw-r--r-- 1 kylem staff 0 1380332088 "May 19 10:31:22 2022" "May 19 10:07:14 2022" "May 19 10:07:14 2022" "May 19 10:00:58 2022" 4096 2720640 0 hg38.15.jf

>>= head -1 hg38.15.jf 
000000447{"alignment":8,"canonical":false,"cmdline":["count","-m","15","-t","5","-s","100M","-L","5","-o","hg38.15.jf","../hg38.NCBI.fa"],"counter_len":4,"exe_path":"/usr/local/bin/jellyfish","format":"binary/sorted","hostname":"Kyles-MacBook-Pro.local","key_len":30,"matrix1":{"c":30,"identity":true,"r":30},"max_reprobe":0,"pwd":"/Users/kylem/Dev/mb/var/genomes/hg38/kmer","reprobes":[1],"size":1073741824,"time":"Thu May 19 09:44:06 2022","val_len":21}?]

With the database in hand, I went to query, like so:
jellyfish query hg38.15.jf AACCTGGGAGGAGGA

But I get an error like:

>>= jellyfish query hg38.15.jf AACCTGGGAGGAGGA
[E::hts_open_format] Failed to open file "P?z" : No such file or directory
libc++abi: terminating with uncaught exception of type std::runtime_error: Can't open SAM file 'P?z'
Abort trap: 6

Oddly, if I re-run the command several times, The contents in the "" change, ex:

>>= jellyfish query hg38.15.jf AACCTGGGAGGAGGA
[E::hts_open_format] Failed to open file "" : No such file or directory
libc++abi: terminating with uncaught exception of type std::runtime_error: Can't open SAM file ''
Abort trap: 6

>>= jellyfish query hg38.15.jf AACCTGGGAGGAGGA
[E::hts_open_format] Failed to open file "P?y" : No such file or directory
libc++abi: terminating with uncaught exception of type std::runtime_error: Can't open SAM file 'P?y'
Abort trap: 6

>>= jellyfish query hg38.15.jf AACCTGGGAGGAGGA
[E::hts_open_format] Failed to open file "?" : No such file or directory
libc++abi: terminating with uncaught exception of type std::runtime_error: Can't open SAM file '?'
Abort trap: 6

I am on the following version:

>>= jellyfish -V
jellyfish 2.3.0

installed via homebrew

I also tried building from source, and get a slightly different error

>>= ./jellyfish query hg38.15.jf AACCTGGGAGGAGGA
R?AH?QH?H?è" : No such file or directory "UH??SPH?H?@?H?
R?AH?QH?H?è'erminating with uncaught exception of type std::runtime_error: Can't open SAM file 'UH??SPH?H?@?H?
Abort trap: 6

[MAfustier]

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

[Kyle McChesney]

@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)

[Joy O'Brien]

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?