danbing-tk: src/aQueryFasta_thread.cpp:1194 int main(int, char**): Assertion ´tfFile´ failed

[dbeyter]

Hi,

I ran the sample command provided for danbing-tk as: samtools fasta -@2 -n $SRS.bam | /$PREFIX/danbing-tk/bin/danbing-tk -gc 80 -ae -kf 4 1 -cth 45 -o $OUT_PREF -k 21 -qs pan -fai /dev/stdin -p $THREADS

and have received: danbing-tk: src/aQueryFasta_thread.cpp:1194 int main(int, char**): Assertion ´tfFile´ failed Aborted (core dumped)

as soon as I run the command above with no other log/progress.

Any help would be appreciated to see why this may be happening. Thank you, Doruk

[joyeuxnoel8]

Hi Doruk,

Thanks for reaching out. Did you happen to place graph index files under a different directory? It's possible to read the indices from a different directory with -qs $PATH_TO_INDEX/pan, assuming you're using the indices we provided.

Thanks, -Tony

[dbeyter]

Hi Tony,

It seems the purpose of the -qs parameter was unclear to me. Thank you for explaining!

Doruk

[jingydz]

Command

(py39) samtools fasta -@2 -n /xxx/vntr/danbing-tk-1.3.1-manuscript/test/input/HG00733.filtered.reads.bam | /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/bam2pe -fai /dev/stdin | /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/danbing-tk -g 50 -k 21 -qs /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//HG00733.rawPB

Log

fname: /dev/stdin danbing-tk: src/aQueryFasta_thread.cpp:1194: int main(int, char**): Assertion `trFile' failed. Aborted (core dumped)

danbing-tk

-qs Prefix for .tr.kmers, .ntr.kmers, *.graph.kmers files

I changed the -qs parameter

Command

(py39) samtools fasta -@2 -n /parastor300/work01/zhangjj/vntr/danbing-tk-1.3.1-manuscript/test/input/HG00733.filtered.reads.bam | /parastor300/work01/zhangjj/vntr/danbing-tk-1.3.1-manuscript//bin/bam2pe -fai /dev/stdin | /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/danbing-tk -g 50 -k 21 -qs /parastor300/work01/zhangjj/vntr/danbing-tk/test/HG00733.rawPB

Log

fname: /dev/stdin use baitDB: 0 extract fasta: 0 interleaved: 0 sim mode: 0 trim mode: 0 augmentation mode: 0 graph threading mode: 1 output alignment: 0 output successfully aligned reads only: 0 k: 21 '# of subsampled kmers in pre-filtering: 4' 'minimal # of matches in pre-filtering: 1' Cthreshold: 0 Rthreshold: 0.5 threading Cthreshold: 50 Thread reads directly (step2: threading) without filtering (step1: kmer-based filtering) fastx: query: /xxx/vntr/danbing-tk/test/HG00733.rawPB.(tr/ntr).kmers

total number of loci in /xxx/vntr/danbing-tk/test/HG00733.rawPB.tr.kmers: 1 deserializing graph.umap danbing-tk: src/aQueryFasta_thread.h:475: void readBinaryGraph(std::vector<std::unordered_map<long unsigned int, unsigned char> >&, std::string&): Assertion `fin' failed. Aborted (core dumped)