DavideGue

Hi Kendell, sorry for the late answer. At the moment I solved the problem by running crispresso2 in amplicon mode. In the next days I will run the commands you...

Here the .pheno file [Flowering_Time.pheno.txt](https://github.com/akcorut/kGWASflow/files/12883334/Flowering_Time.pheno.txt) Thank you for your help, Davide

Hi, I removed the samples with missing genotypes and it apparently solved that issue. However, I got a different error message now: [Thu Oct 12 14:20:04 2023] Job 2972: Running...

Here the content of results/kmers_gwas/Flowering_Time/kmers/ best_pvals pheno.31.P31.bed pheno.54.P54.fam pheno.78.P78.bed output pheno.31.P31.bim pheno.54.P54.fam.orig pheno.78.P78.bim pheno.0.phenotype_value.bed pheno.31.P31.fam pheno.55.P55.bed pheno.78.P78.fam pheno.0.phenotype_value.bim pheno.31.P31.fam.orig pheno.55.P55.bim pheno.78.P78.fam.orig pheno.0.phenotype_value.fam pheno.32.P32.bed pheno.55.P55.fam pheno.79.P79.bed pheno.0.phenotype_value.fam.orig pheno.32.P32.bim pheno.55.P55.fam.orig pheno.79.P79.bim pheno.100.P100.bed...

Hi @akcorut yes the output folder is empty! Which version of gemma does the pipeline use? I noticed problems running gemma v0.96, while I can run succesfully gemma v0.98 on...

Thank you for your reply. However, after following the suggestions in #712 we still get error message as below: executor > slurm (88) [4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔...

Yes, the test profile works well. Attached the two logs requested [command.log](https://github.com/user-attachments/files/22659964/command.log) [output (4) 1.log](https://github.com/user-attachments/files/22659965/output.4.1.log)