Open exkahn opened 1 month ago
Hi @exkahn, thanks for opening an issue. If I understand, other the concat_gvcfs
step works for other samples?
Yes, kind of -- it worked for the first three samples. However, when I took out EucyKris_LasFloCk_90_En_187 (the sample where the error is happening), two different samples caused the same error.
Hmm. This is a little tricky to debug without any error logs, unfortunately. One common problem with concat steps is running out of temp space. You might try setting bigtmp in the config to a local directory that you know has lots of space and see if that helps.
Hi @exkahn, we've updated snpArcher to better capture the logs from these rules. If you pull the latest changes and rerun that may give us some more info to diagnose.
Hi, I've been trying to run snpArcher on genomic resequencing data, but I've been running into an error with the concat_gvcfs step.
The command I'm using is
The end of the .snakemake/log file lists an error that looks like this:
Activating conda environment: .snakemake/conda/b78e203ca0a7037a682091b03d0f69dd_ [Tue Jul 30 16:00:53 2024] Error in rule concat_gvcfs: jobid: 14 input: results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0000.raw.g.vcf.gz, results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0001.raw.g.vcf.gz, results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0002.raw.g.vcf.gz, results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0003.raw.g.vcf.gz, [...more .raw.g.vcf.gz files to 0021...] results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0000.raw.g.vcf.gz.tbi, results/GCA_026437355.1/interval_gvcfs/EucyKris_LasFloCk_90_En_187/0001.raw.g.vcf.gz.tbi, [...more .raw.g.vcf.gz.tbi files to 0021] log: logs/GCA_026437355.1/concat_gvcfs/EucyKris_LasFloCk_90_En_187.txt (check log file(s) for error details) conda-env: /data/home/miabrecht/CCGPTidewaterGoby/snpArcher/.snakemake/conda/b78e203ca0a7037a682091b03d0f69dd shell:
This follows several identical steps with different samples which seem successful. The log files in logs/concat_gvcfs are all empty .txt files. Here is my config file, converted to .txt: config.txt, and I haven't been using a profile yaml file. I'd appreciate any help, thanks!