search

akcorut / kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
https://github.com/akcorut/kGWASflow/wiki
MIT License
28 stars 8 forks source link

Error in rule run_kmers_gwas #24

Open DavideGue opened 11 months ago

DavideGue commented 11 months ago

Hi @akcorut , I am running kGWASflow on a VM hosted on our server with 7TB Hard Disk and 180 G RAM. I got this message: [Thu Oct 12 01:53:07 2023] Job 2972: Running k-mers based GWAS on /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno... Reason: Missing output files: results/kmers_gwas/Flowering_Time/kmers/pass_threshold_5per; Input files updated by another job: results/kmers_table/kmers_table.table, results/kmers_table/kmers_table.kinship, scripts/external/kmers_gwas/kmers_gwas.py

Activating conda environment: .snakemake/conda/66a0fa76bc7c3da7cd9f3a46e7e64c95_ [Thu Oct 12 01:53:22 2023] Error in rule run_kmers_gwas: jobid: 2972 input: scripts/external/kmers_gwas/kmers_gwas.py, /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno, results/kmers_table/kmers_table.table, results/kmers_table/kmers_table.kinship output: results/kmers_gwas/Flowering_Time/kmers/pass_threshold_5per log: logs/kmers_gwas/Flowering_Time/Flowering_Time_kmers_gwas_run.log (check log file(s) for error details) conda-env: /mnt/Data-out/kgwasflowwd/.snakemake/conda/66a0fa76bc7c3da7cd9f3a46e7e64c95 shell:

    export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

    rm -r results/kmers_gwas/Flowering_Time

    python2 scripts/external/kmers_gwas/kmers_gwas.py          --min_data_points 30         --pheno /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno         --kmers_table results/kmers_table/kmers_table         --kmers_number 10001         --permutations 100         --maf 0.05 --mac 5         -l 31 -p 12         --outdir results/kmers_gwas/Flowering_Time >>logs/kmers_gwas/Flowering_Time/Flowering_Time_kmers_gwas_run.log 2>&1

    (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 Error! The Snakemake workflow aborted. Complete log: .snakemake/log/2023-10-03T162604.308859.snakemake.log ERROR:root:Error running Snakemake: Command '['snakemake', '--use-conda', '--conda-frontend', 'conda', '--cores', '12', '--snakefile', '/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/Snakefile', '--rerun-triggers', 'mtime', 'params', 'input', 'software-env', 'code']' returned non-zero exit status 1.

Attached you can find the log file logs/kmers_gwas/Flowering_Time/Flowering_Time_kmers_gwas_run.log Flowering_Time_kmers_gwas_run.LOG

akcorut commented 11 months ago

Hi @DavideGue,

This error seems to be related to the phenotype file. Do you mind sharing your .pheno file with me so I can have a look?

Best, Kivanc

DavideGue commented 11 months ago

Here the .pheno file Flowering_Time.pheno.txt Thank you for your help, Davide

akcorut commented 11 months ago

Okay, it looks like there is one missing phenotype information for your accession WB-359. If you remove the row with the missing pheno (WB-359) and run the pipeline again, it should work without a problem. 

WB-355  86.411
WB-356  78.509
WB-357  82.411
WB-359  
WB-360  79.404
WB-361  74.411

WB-153 seems to have no phenotype information as well.

In the future, make sure to check your .pheno files and simply remove any samples with missing phenotype information from the .pheno file.

Hope this will solve the issue.

Kivanc

DavideGue commented 11 months ago

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 k-mers based GWAS on /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno... Reason: Missing output files: results/kmers_gwas/Flowering_Time/kmers/pass_threshold_5per

Activating conda environment: .snakemake/conda/66a0fa76bc7c3da7cd9f3a46e7e64c95_ [Thu Oct 12 15:41:52 2023] Error in rule run_kmers_gwas: jobid: 2972 input: scripts/external/kmers_gwas/kmers_gwas.py, /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno, results/kmers_table/kmers_table.table, results/kmers_table/kmers_table.kinship output: results/kmers_gwas/Flowering_Time/kmers/pass_threshold_5per log: logs/kmers_gwas/Flowering_Time/Flowering_Time_kmers_gwas_run.log (check log file(s) for error details) conda-env: /mnt/Data-out/kgwasflowwd/.snakemake/conda/66a0fa76bc7c3da7cd9f3a46e7e64c95 shell:

    export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

    rm -r results/kmers_gwas/Flowering_Time

    python2 scripts/external/kmers_gwas/kmers_gwas.py          --min_data_points 30         --pheno /mnt/Data-out/kgwasflow_wd/Flowering_Time.pheno         --kmers_table results/kmers_table/kmers_table         --kmers_number 10001         --permutations 100         --maf 0.05 --mac 5         -l 31 -p 12         --outdir results/kmers_gwas/Flowering_Time >>logs/kmers_gwas/Flowering_Time/Flowering_Time_kmers_gwas_run.log 2>&1

    (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 Error! The Snakemake workflow aborted. Complete log: .snakemake/log/2023-10-12T141754.479754.snakemake.log ERROR:root:Error running Snakemake: Command '['snakemake', '--use-conda', '--conda-frontend', 'conda', '--cores', '12', '--snakefile', '/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/Snakefile', '--rerun-triggers', 'mtime', 'params', 'input', 'software-env', 'code']' returned non-zero exit status 1.

Here log files:

log_file.txt Flowering_Time_kmers_gwas_run.log.txt

I hope that what I add below can help: I also tried to run kmer_gwas.py from https://github.com/voichek/kmersGWAS/tree/master using the docker image at the link he provides on its giuthub page. In this case I used the k-mers table generated by kgwasflow. Doing this I got the following error message: root@3613c691355a:/app# python2.7 kmers_gwas.py --pheno ./manual_kgwas/pheno.phenotypes --kmers_table ./manual_kgwas/kmers_table -l 31 -p 4 --outdir ./results affective MAF = 0.05 /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /app/external_programs/gemma_0_96: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "kmers_gwas.py", line 278, in main() File "kmers_gwas.py", line 247, in main th_5per = get_threshold_from_perm(res, "P", args.n_permutations, 0.05) File "/app/src/py/functions.py", line 110, in get_threshold_from_perm pvals.append(best_pvals[prefix + str(i)]) KeyError: 'P1'

akcorut commented 11 months ago

Hi @DavideGue,

Can you share the content of results/kmers_gwas/Flowering_Time/kmers/. You can just name the files that exist in that directory. This is most likely an issue with kmersGWAS and GEMMA, but I will try to find a solution for you.

Unfortunately, I cannot really comment on the issues with that docker image because it is not part of the kGWASflow pipeline.

Best, Kivanc

DavideGue commented 11 months ago

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 pheno.32.P32.fam pheno.56.P56.bed pheno.79.P79.fam pheno.100.P100.bim pheno.32.P32.fam.orig pheno.56.P56.bim pheno.79.P79.fam.orig pheno.100.P100.fam pheno.33.P33.bed pheno.56.P56.fam pheno.7.P7.bed pheno.100.P100.fam.orig pheno.33.P33.bim pheno.56.P56.fam.orig pheno.7.P7.bim pheno.10.P10.bed pheno.33.P33.fam pheno.57.P57.bed pheno.7.P7.fam pheno.10.P10.bim pheno.33.P33.fam.orig pheno.57.P57.bim pheno.7.P7.fam.orig pheno.10.P10.fam pheno.34.P34.bed pheno.57.P57.fam pheno.80.P80.bed pheno.10.P10.fam.orig pheno.34.P34.bim pheno.57.P57.fam.orig pheno.80.P80.bim pheno.11.P11.bed pheno.34.P34.fam pheno.58.P58.bed pheno.80.P80.fam pheno.11.P11.bim pheno.34.P34.fam.orig pheno.58.P58.bim pheno.80.P80.fam.orig pheno.11.P11.fam pheno.35.P35.bed pheno.58.P58.fam pheno.81.P81.bed pheno.11.P11.fam.orig pheno.35.P35.bim pheno.58.P58.fam.orig pheno.81.P81.bim pheno.12.P12.bed pheno.35.P35.fam pheno.59.P59.bed pheno.81.P81.fam pheno.12.P12.bim pheno.35.P35.fam.orig pheno.59.P59.bim pheno.81.P81.fam.orig pheno.12.P12.fam pheno.36.P36.bed pheno.59.P59.fam pheno.82.P82.bed pheno.12.P12.fam.orig pheno.36.P36.bim pheno.59.P59.fam.orig pheno.82.P82.bim pheno.13.P13.bed pheno.36.P36.fam pheno.5.P5.bed pheno.82.P82.fam pheno.13.P13.bim pheno.36.P36.fam.orig pheno.5.P5.bim pheno.82.P82.fam.orig pheno.13.P13.fam pheno.37.P37.bed pheno.5.P5.fam pheno.83.P83.bed pheno.13.P13.fam.orig pheno.37.P37.bim pheno.5.P5.fam.orig pheno.83.P83.bim pheno.14.P14.bed pheno.37.P37.fam pheno.60.P60.bed pheno.83.P83.fam pheno.14.P14.bim pheno.37.P37.fam.orig pheno.60.P60.bim pheno.83.P83.fam.orig pheno.14.P14.fam pheno.38.P38.bed pheno.60.P60.fam pheno.84.P84.bed pheno.14.P14.fam.orig pheno.38.P38.bim pheno.60.P60.fam.orig pheno.84.P84.bim pheno.15.P15.bed pheno.38.P38.fam pheno.61.P61.bed pheno.84.P84.fam pheno.15.P15.bim pheno.38.P38.fam.orig pheno.61.P61.bim pheno.84.P84.fam.orig pheno.15.P15.fam pheno.39.P39.bed pheno.61.P61.fam pheno.85.P85.bed pheno.15.P15.fam.orig pheno.39.P39.bim pheno.61.P61.fam.orig pheno.85.P85.bim pheno.16.P16.bed pheno.39.P39.fam pheno.62.P62.bed pheno.85.P85.fam pheno.16.P16.bim pheno.39.P39.fam.orig pheno.62.P62.bim pheno.85.P85.fam.orig pheno.16.P16.fam pheno.3.P3.bed pheno.62.P62.fam pheno.86.P86.bed pheno.16.P16.fam.orig pheno.3.P3.bim pheno.62.P62.fam.orig pheno.86.P86.bim pheno.17.P17.bed pheno.3.P3.fam pheno.63.P63.bed pheno.86.P86.fam pheno.17.P17.bim pheno.3.P3.fam.orig pheno.63.P63.bim pheno.86.P86.fam.orig pheno.17.P17.fam pheno.40.P40.bed pheno.63.P63.fam pheno.87.P87.bed pheno.17.P17.fam.orig pheno.40.P40.bim pheno.63.P63.fam.orig pheno.87.P87.bim pheno.18.P18.bed pheno.40.P40.fam pheno.64.P64.bed pheno.87.P87.fam pheno.18.P18.bim pheno.40.P40.fam.orig pheno.64.P64.bim pheno.87.P87.fam.orig pheno.18.P18.fam pheno.41.P41.bed pheno.64.P64.fam pheno.88.P88.bed pheno.18.P18.fam.orig pheno.41.P41.bim pheno.64.P64.fam.orig pheno.88.P88.bim pheno.19.P19.bed pheno.41.P41.fam pheno.65.P65.bed pheno.88.P88.fam pheno.19.P19.bim pheno.41.P41.fam.orig pheno.65.P65.bim pheno.88.P88.fam.orig pheno.19.P19.fam pheno.42.P42.bed pheno.65.P65.fam pheno.89.P89.bed pheno.19.P19.fam.orig pheno.42.P42.bim pheno.65.P65.fam.orig pheno.89.P89.bim pheno.1.P1.bed pheno.42.P42.fam pheno.66.P66.bed pheno.89.P89.fam pheno.1.P1.bim pheno.42.P42.fam.orig pheno.66.P66.bim pheno.89.P89.fam.orig pheno.1.P1.fam pheno.43.P43.bed pheno.66.P66.fam pheno.8.P8.bed pheno.1.P1.fam.orig pheno.43.P43.bim pheno.66.P66.fam.orig pheno.8.P8.bim pheno.20.P20.bed pheno.43.P43.fam pheno.67.P67.bed pheno.8.P8.fam pheno.20.P20.bim pheno.43.P43.fam.orig pheno.67.P67.bim pheno.8.P8.fam.orig pheno.20.P20.fam pheno.44.P44.bed pheno.67.P67.fam pheno.90.P90.bed pheno.20.P20.fam.orig pheno.44.P44.bim pheno.67.P67.fam.orig pheno.90.P90.bim pheno.21.P21.bed pheno.44.P44.fam pheno.68.P68.bed pheno.90.P90.fam pheno.21.P21.bim pheno.44.P44.fam.orig pheno.68.P68.bim pheno.90.P90.fam.orig pheno.21.P21.fam pheno.45.P45.bed pheno.68.P68.fam pheno.91.P91.bed pheno.21.P21.fam.orig pheno.45.P45.bim pheno.68.P68.fam.orig pheno.91.P91.bim pheno.22.P22.bed pheno.45.P45.fam pheno.69.P69.bed pheno.91.P91.fam pheno.22.P22.bim pheno.45.P45.fam.orig pheno.69.P69.bim pheno.91.P91.fam.orig pheno.22.P22.fam pheno.46.P46.bed pheno.69.P69.fam pheno.92.P92.bed pheno.22.P22.fam.orig pheno.46.P46.bim pheno.69.P69.fam.orig pheno.92.P92.bim pheno.23.P23.bed pheno.46.P46.fam pheno.6.P6.bed pheno.92.P92.fam pheno.23.P23.bim pheno.46.P46.fam.orig pheno.6.P6.bim pheno.92.P92.fam.orig pheno.23.P23.fam pheno.47.P47.bed pheno.6.P6.fam pheno.93.P93.bed pheno.23.P23.fam.orig pheno.47.P47.bim pheno.6.P6.fam.orig pheno.93.P93.bim pheno.24.P24.bed pheno.47.P47.fam pheno.70.P70.bed pheno.93.P93.fam pheno.24.P24.bim pheno.47.P47.fam.orig pheno.70.P70.bim pheno.93.P93.fam.orig pheno.24.P24.fam pheno.48.P48.bed pheno.70.P70.fam pheno.94.P94.bed pheno.24.P24.fam.orig pheno.48.P48.bim pheno.70.P70.fam.orig pheno.94.P94.bim pheno.25.P25.bed pheno.48.P48.fam pheno.71.P71.bed pheno.94.P94.fam pheno.25.P25.bim pheno.48.P48.fam.orig pheno.71.P71.bim pheno.94.P94.fam.orig pheno.25.P25.fam pheno.49.P49.bed pheno.71.P71.fam pheno.95.P95.bed pheno.25.P25.fam.orig pheno.49.P49.bim pheno.71.P71.fam.orig pheno.95.P95.bim pheno.26.P26.bed pheno.49.P49.fam pheno.72.P72.bed pheno.95.P95.fam pheno.26.P26.bim pheno.49.P49.fam.orig pheno.72.P72.bim pheno.95.P95.fam.orig pheno.26.P26.fam pheno.4.P4.bed pheno.72.P72.fam pheno.96.P96.bed pheno.26.P26.fam.orig pheno.4.P4.bim pheno.72.P72.fam.orig pheno.96.P96.bim pheno.27.P27.bed pheno.4.P4.fam pheno.73.P73.bed pheno.96.P96.fam pheno.27.P27.bim pheno.4.P4.fam.orig pheno.73.P73.bim pheno.96.P96.fam.orig pheno.27.P27.fam pheno.50.P50.bed pheno.73.P73.fam pheno.97.P97.bed pheno.27.P27.fam.orig pheno.50.P50.bim pheno.73.P73.fam.orig pheno.97.P97.bim pheno.28.P28.bed pheno.50.P50.fam pheno.74.P74.bed pheno.97.P97.fam pheno.28.P28.bim pheno.50.P50.fam.orig pheno.74.P74.bim pheno.97.P97.fam.orig pheno.28.P28.fam pheno.51.P51.bed pheno.74.P74.fam pheno.98.P98.bed pheno.28.P28.fam.orig pheno.51.P51.bim pheno.74.P74.fam.orig pheno.98.P98.bim pheno.29.P29.bed pheno.51.P51.fam pheno.75.P75.bed pheno.98.P98.fam pheno.29.P29.bim pheno.51.P51.fam.orig pheno.75.P75.bim pheno.98.P98.fam.orig pheno.29.P29.fam pheno.52.P52.bed pheno.75.P75.fam pheno.99.P99.bed pheno.29.P29.fam.orig pheno.52.P52.bim pheno.75.P75.fam.orig pheno.99.P99.bim pheno.2.P2.bed pheno.52.P52.fam pheno.76.P76.bed pheno.99.P99.fam pheno.2.P2.bim pheno.52.P52.fam.orig pheno.76.P76.bim pheno.99.P99.fam.orig pheno.2.P2.fam pheno.53.P53.bed pheno.76.P76.fam pheno.9.P9.bed pheno.2.P2.fam.orig pheno.53.P53.bim pheno.76.P76.fam.orig pheno.9.P9.bim pheno.30.P30.bed pheno.53.P53.fam pheno.77.P77.bed pheno.9.P9.fam pheno.30.P30.bim pheno.53.P53.fam.orig pheno.77.P77.bim pheno.9.P9.fam.orig pheno.30.P30.fam pheno.54.P54.bed pheno.77.P77.fam pheno.tested_kmers pheno.30.P30.fam.orig pheno.54.P54.bim pheno.77.P77.fam.orig Best, Davide

akcorut commented 11 months ago

Hi @DavideGue,

Is the output/ folder empty?

DavideGue commented 11 months ago

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 my machine. Could that be the problem?