Swiss Army Knife not generating outputs (merged .bed file)?

• 

  Alexandra Lee DNAnexus Team

  • 14 April 2023 22:16

  Hi Ilaria,

   

  I don?t think you need to use the mounted files (i.e. `/mnt/project/`) with the -icmd params for your command. So you can use `ad_risk_by_proxy_wes.phe` instead of `/mnt/project/ad_risk_by_proxy_wes.phe`.

   

  There also looks like there is a minor typo in your `run_merge` command. You have ?files_to_merge.txt? and ?files_to_merge_.txt?

   

  I was able to successfully run SAK after making these adjustments.

   

  Also just so you know, there is an updated GWAS tutorial here: https://www.youtube.com/watch?v=jN25SIGZFDE

   

  And the corresponding code is available here: https://github.com/dnanexus/UKB_RAP/tree/main/end_to_end_gwas_phewas

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• 

  Former User of DNAx Community_42

  • 17 April 2023 17:12

  Hi Alexandra, thank you so much! I still have not been able to successfully run SAK.

   

  Here is the code I am running now:

   

  run_merge="cp /mnt/project/Bulk/Genotype\ Results/Genotype\ calls/ukb22418_c[1-9]* . ;\

    ls *.bed | sed -e 's/.bed//g'> files_to_merge_.txt; \

    plink --merge-list files_to_merge_.txt --make-bed --autosome-xy --out

  ukb22418_c1_22_v2_merged;\

    rm files_to_merge.txt;"

     

  dx run swiss-army-knife\

    -iin='ad_risk_by_proxy_wes.phe' \

    -icmd='${run_merge}' --tag='Step1'\

    --instance-type "mem1_ssd1_v2_x16"\

    --destination='/mnt/project/Data/' --brief --yes

   

  Best,

  Ilaria

   

   

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• 

  Alexandra Lee DNAnexus Team

  • 18 April 2023 17:28

  Here is what I did that worked:

   

  run_merge=?cp /mnt/project/Bulk/Genotype\ Results/Genotype\ calls/ukb22418_c[1-9]* . ; ls *.bed | sed -e 's/.bed//g'> files_to_merge.txt; plink --merge-list files_to_merge.txt --make-bed --autosome-xy --out ukb22418_c1_22_v2_merged; rm files_to_merge.txt;?

   

  dx run swiss-army-knife -iin="/<file path>/ad_risk_by_proxy_wes.phe" -icmd="${run_merge}" --tag="Step1" --instance-type "mem1_ssd1_v2_x16" --destination="/<file path without mnt>/" --brief --yes

   

  I'm not sure if its the destination params using dxfuse, I would need to see the error message.

   

  Hope this helps

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• 

  Former User of DNAx Community_42

  • 19 April 2023 17:17

  Thank you so much!

   

  This syntax worked for me, but now I am getting a permission error.  

  I really appreciate all your assistance.

  Best,

  Ilaria

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• 

  Alexandra Lee DNAnexus Team

  • 19 April 2023 22:55

  It looks like you're using `/mnt/project/ in your `-iin` params. Maybe try removing the mounted file path

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