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ChaissonLab / danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction
BSD 3-Clause "New" or "Revised" License
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Segmentation fault when checking the environment with testing samples #25

Open Xgiintghhuabi302 opened 1 year ago

Xgiintghhuabi302 commented 1 year ago

Dear ChaissonLab, I am trying to check my environment by running on the testing samples with command: snakemake -p -s ../pipeline/GoodPanGenomeGraph.snakefile -j 4 --rerun-incomplete --output-wait 5 and I encountered some problems in this line: /home/txren/my_path/danbing_tk/danbing-tk/bin/ktools serialize /home/txren/my_path/danbing_tk/danbing-tk/test/output/pan with the err: reading kmers from /home/txren/my_path/danbing_tk/danbing-tk/test/output/pan.graph.kmers /usr/bin/bash: line 4: 1863431 Segmentation fault (core dumped) /home/txren/my_path/danbing_tk/danbing-tk/bin/ktools serialize /home/txren/my_path/danbing_tk/danbing-tk/test/output/pan Could you help me with this issue?

jingydz commented 1 year ago

Hi, I also encountered the same problem. Have you solved it?

Command

snakemake -p -s ../pipeline/GoodPanGenomeGraph.snakefile -j 4 --rerun-incomplete --output-wait 3

Log

Building DAG of jobs... ... cd /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/ ulimit -c 20000 module load gcc

/xxx/vntr/danbing-tk-1.3.1-manuscript//bin/ktools serialize /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//pan /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/ktools ksi pan.tr.kmers >/xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//pan.tr.ksi

ModuleCmd_Load.c(204):ERROR:105: Unable to locate a modulefile for 'gcc' reading kmers from /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//pan.graph.kmers /bin/bash: line 5: 23822 Segmentation fault (core dumped) /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/ktools serialize /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//pan [Fri Apr 14 15:00:33 2023] Error in rule GenSerializedGraphAndIndex: jobid: 11 input: /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.tr.kmers, /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.ntr.kmers, /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.graph.kmers output: /parastor300/work01/zhangjj/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.graph.umap, /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.kmerDBi.umap, /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/pan.kmerDBi.vv shell:

cd /xxx/vntr/danbing-tk-1.3.1-manuscript/test/output/ ulimit -c 20000 module load gcc

/xxx/vntr/danbing-tk-1.3.1-manuscript//bin/ktools serialize /parastor300/work01/zhangjj/vntr/danbing-tk-1.3.1-manuscript/test/output//pan /xxx/vntr/danbing-tk-1.3.1-manuscript//bin/ktools ksi pan.tr.kmers >/xxx/vntr/danbing-tk-1.3.1-manuscript/test/output//pan.tr.ksi

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-04-14T150025.521279.snakemake.log

Xgiintghhuabi302 commented 1 year ago

@jingydz i haven't fixed the issue, but i note that the test was built on v1.0, so i roll back to the v1.0 and the fault didn't appear. Hope this helps you.

joyeuxnoel8 commented 1 year ago

Hi @Xgiintghhuabi302 and @jingydz,

Thanks for reaching out. I've just fixed the bug in the latest commit 4b64113de14d63a012b0c415a0255ccdd330488e. The reason is that genPanKmers did not write kmer names but ktools serialize require kmer names. Let me know if the issue exists or if you run into other issues.

Cheers, -Tony