Error Segmentation fault

[ZhezhiGao]

Hi there, thanks for developing the excellent tool. I ran into an error when testing the sample NA12718,
ctyper -i NA12718.final.cram -m ../HprcCpcHgsvc_cmr_matrix.txt -o ctyper.out > log.txt
Segmentation fault (core dumped)
Could you kindly resolve this rather naive question?

[Walfred-MA]

Hi there, thanks for developing the excellent tool. I ran into an error when testing the sample NA12718,
ctyper -i NA12718.final.cram -m ../HprcCpcHgsvc_cmr_matrix.txt -o ctyper.out > log.txt
Segmentation fault (core dumped)
Could you kindly resolve this rather naive question?

Can you double check if you have cram.crai file and matrix.txt.index

[ZhezhiGao]

Thanks for the prompt reply. I downloaded the input files from Zenodo and used md5sum to ensure the files were correct. My directory contains the following files:
HprcCpcHgsvc_cmr_matrix.txt HprcCpcHgsvc_cmr_matrix.txt.bgd HprcCpcHgsvc_cmr_matrix.txt.index PangenomeAlleles_annotationfix.tsv NA12718.final.cram NA12718.final.cram.crai
but I still ran into this error.

Best,
Zhezhi

[Walfred-MA]

Can you also share your command ?

[ZhezhiGao]

Sure.
I installed ctyper as:
(base) s1024226003@node02:~/ctyper$ conda create -n ctyper_env -c conda-forge -c bioconda ctyper
(base) s1024226003@node02:~/ctyper$ conda activate ctyper_env

It seems to be installed successfully:

(ctyper_env) s1024226003@node02:~/ctyper$ ctyper
Usage: CTyper [options]

Options:
  -i, --input <file>         Input NGS file, allows CRAM(indexed), BAM(indexed), SAM, FASTQ and FASTA formats
  -I, --Inputs <file>        File with a list of input files
  -m, --matrix <file>        Path to the matrix database, need to come with its index file 
  -o, --output <file>        Output file
  -O, --Outputs <file>       File with a list of output files
  -n, --nthreads <number>    Number of threads to use (default: 1) 
  -N, --Nsubthreads <number> Number of sub-threads (default: 1) 
  -d, --depth <value>        Predetermined depth value, not compatible with -b options
  -D, --Depth <file>         File with a list of predetermined depth values, not compatible with -b options
  -b, --background <file>    Background k-mer file, used to determine NGS coverage, not compatible with -d/-D options 
  -c, --corr <0/1>           Set correction for biased k-mer option for NGS data (default: 0)
  -h, --help                 Show this help message

And then downloaded and unzipped files:

(ctyper_env) s1024226003@node02:~/ctyper$ wget "https://zenodo.org/records/16340156/files/HprcCpcHgsvc_cmr_matrix.txt.gz"
(ctyper_env) s1024226003@node02:~/ctyper$ wget "https://zenodo.org/records/16340156/files/HprcCpcHgsvc_cmr_matrix.txt.index"
(ctyper_env) s1024226003@node02:~/ctyper$ wget "https://zenodo.org/records/16340156/files/HprcCpcHgsvc_cmr_matrix.txt.bgd"
(ctyper_env) s1024226003@node02:~/ctyper$ wget "https://zenodo.org/records/16340156/files/PangenomeAlleles_annotationfix.tsv.gz"
(ctyper_env) s1024226003@node02:~/ctyper$ gunzip HprcCpcHgsvc_cmr_matrix.txt.gz
(ctyper_env) s1024226003@node02:~/ctyper$ gunzip PangenomeAlleles_annotationfix.tsv.gz
(ctyper_env) s1024226003@node02:~/ctyper$ wget "ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239480/NA12718.final.cram"
(ctyper_env) s1024226003@node02:~/ctyper$ wget "ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239480/NA12718.final.cram.crai"

Then I ran ctyper as recommended, here is the error:

(ctyper_env) s1024226003@node02:~/ctyper$ ctyper -i NA12718.final.cram -m HprcCpcHgsvc_cmr_matrix.txt -o ctyper.out > log.txt 
Segmentation fault (core dumped)

[Walfred-MA]

Maybe there is version conflicts. Can you try with the github code and compile from the source. If this is the case, I will let mark update the conda... Best

[ZhezhiGao]

OK, I'll try.

Best,
Zhezhi