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GeneNetwork (2nd generation)
http://gn2.genenetwork.org/
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Pylmm error #272

Closed jdjentsch closed 6 years ago

jdjentsch commented 6 years ago

I encountered the following error when trying to utilize Pylmm analyses on dataset JBagley_Sucrose_trait1

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 1:58PM UTC Jan 19, 2018) ERROR: failed on /usr/local/guix-profiles/gn2-2.10rc4/bin/pylmm_redis --key pylmm:input:7a04bc96-eb0c-483a-ab06-62887aaab22d --species other (error) File "/home/production/gene/wqflask/utility/external.py", line 9, in shell raise Exception("ERROR: failed on "+command)

pjotrp commented 6 years ago

@zsloan can you take a look?

robwwilliams commented 6 years ago

Dear David,

Just some initial analysis/diagnosis. These data have been entered into both the mouse BXD and mouse MDP groups.

Trait Data and Analysis for 19387JBagley_Sucrose_trait1 (entered as part of BXD Group)

  1. Trait 19387 is entered under BXD with 24 BXDs and 70 Other (92 total, since B6 and D2 in both groups)

  2. Interval mapping works but is only using BXD data

  3. pyLMM mapping works using BXD data (peak on Chr 2)

  4. GEMMA with LOCO works using BXD data (peak again on Chr 2)

Trait Data and Analysis for 50187 (same data but now MDP Group) JBagley_Sucrose_trait1

  1. Trait 50187 interval mapping works but ugly output with JPEG artifact. Peak on Chr 18. Probably using all 92 strains.

  2. pyLMM mapping works using BXD data (peak on Chr 2) generates this error

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 3:42PM UTC Jan 19, 2018) ERROR: failed on /usr/local/guix-profiles/gn2-2.10rc4/bin/pylmm_redis --key pylmm:input:421c44b5-a610-4aed-a7b3-640a890d31c5 --species other (error) File "/home/production/gene/wqflask/utility/external.py", line 9, in shell raise Exception("ERROR: failed on "+command)

  1. GEMMA with LOCO generates this error

GeneNetwork error: [Errno 2] No such file or directory: u'/tmp/2f6a8998cc0b2feebd1627352a6fc2b97a4f9027.1.assoc.txt.assoc.txt')

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db

http://gn2.genenetwork.org/marker_regression ( 3:43PM UTC Jan 19, 2018) [Errno 2] No such file or directory: u'/tmp/2f6a8998cc0b2feebd1627352a6fc2b97a4f9027.1.assoc.txt.assoc.txt' (error) File "/home/production/gene/wqflask/wqflask/marker_regression/gemma_mapping.py", line 226, in parse_loco_output with open(this_file) as output_file:

On Fri, Jan 19, 2018 at 7:59 AM, jdjentsch notifications@github.com wrote:

I encountered the following error when trying to utilize Pylmm analyses on dataset JBagley_Sucrose_trait1

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 1:58PM UTC Jan 19, 2018) ERROR: failed on /usr/local/guix-profiles/gn2-2.10rc4/bin/pylmm_redis --key pylmm:input:7a04bc96-eb0c-483a-ab06-62887aaab22d --species other (error) File "/home/production/gene/wqflask/utility/external.py", line 9, in shell raise Exception("ERROR: failed on "+command)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/272, or mute the thread https://github.com/notifications/unsubscribe-auth/ALva_Mrx4BU7jLnnqqP7HvxXwtvRLEhYks5tMJ_RgaJpZM4Rkg1U .

-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics 71 S Manassas St, Memphis TN 38163 University of Tennessee Health Science Center Office 901 448-7050 CELL 901 604 4752 Office: Translational Science Research Building, Room 407 EMAIL: rwilliams@uthsc.edu Alternative email: labwilliams@gmail.com SKYPE: robwwilliams

zsloan commented 6 years ago

I don't know about PYLMM (maybe it's the same problem I describe below, but I don't know how to check), but the GEMMA issue might be because it isn't generating a kinship matrix. When I run the script to generate kinship matrices for all our genotype files, it says "Segmentation fault (core dumped)" when it tries to generate the kinship matrix for MDP. For some reason this error does not occur for the mm8 MDP genofile.

The only possible reason I can think of is that the non-mm8 MDP bimbam file has entire columns of NAs (which isn't the case for the mm8 one). I can try editing the script that converts .geno files to bimbam to ignore columns of NAs (this might be easier said than done, though, since it wouldn't know if a column is all NAs until already looping through all rows), but I'm not sure if that would fix the issue or possibly cause problems elsewhere.

On Fri, Jan 19, 2018 at 9:44 AM, robwwilliams notifications@github.com wrote:

Dear David,

Just some initial analysis/diagnosis. These data have been entered into both the mouse BXD and mouse MDP groups.

Trait Data and Analysis for 19387JBagley_Sucrose_trait1 (entered as part of BXD Group)

  1. Trait 19387 is entered under BXD with 24 BXDs and 70 Other (92 total, since B6 and D2 in both groups)

  2. Interval mapping works but is only using BXD data

  3. pyLMM mapping works using BXD data (peak on Chr 2)

  4. GEMMA with LOCO works using BXD data (peak again on Chr 2)

Trait Data and Analysis for 50187 (same data but now MDP Group) JBagley_Sucrose_trait1

  1. Trait 50187 interval mapping works but ugly output with JPEG artifact. Peak on Chr 18. Probably using all 92 strains.

  2. pyLMM mapping works using BXD data (peak on Chr 2) generates this error

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 3:42PM UTC Jan 19, 2018) ERROR: failed on /usr/local/guix-profiles/gn2-2.10rc4/bin/pylmm_redis --key pylmm:input:421c44b5-a610-4aed-a7b3-640a890d31c5 --species other (error) File "/home/production/gene/wqflask/utility/external.py", line 9, in shell raise Exception("ERROR: failed on "+command)

  1. GEMMA with LOCO generates this error

GeneNetwork error: [Errno 2] No such file or directory: u'/tmp/2f6a8998cc0b2feebd1627352a6fc2b97a4f9027.1.assoc.txt.assoc.txt')

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 3:43PM UTC Jan 19, 2018) [Errno 2] No such file or directory: u'/tmp/2f6a8998cc0b2feebd1627352a6fc2b97a4f9027.1.assoc.txt.assoc.txt' (error) File "/home/production/gene/wqflask/wqflask/marker_ regression/gemma_mapping.py", line 226, in parse_loco_output with open(this_file) as output_file:

On Fri, Jan 19, 2018 at 7:59 AM, jdjentsch notifications@github.com wrote:

I encountered the following error when trying to utilize Pylmm analyses on dataset JBagley_Sucrose_trait1

GeneNetwork penguin:gene:2.10rc3-production-f6ad049db http://gn2.genenetwork.org/marker_regression ( 1:58PM UTC Jan 19, 2018) ERROR: failed on /usr/local/guix-profiles/gn2-2.10rc4/bin/pylmm_redis --key pylmm:input:7a04bc96-eb0c-483a-ab06-62887aaab22d --species other (error) File "/home/production/gene/wqflask/utility/external.py", line 9, in shell raise Exception("ERROR: failed on "+command)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/272, or mute the thread https://github.com/notifications/unsubscribe-auth/ALva_ Mrx4BU7jLnnqqP7HvxXwtvRLEhYks5tMJ_RgaJpZM4Rkg1U .

-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics 71 S Manassas St, Memphis TN 38163 https://maps.google.com/?q=71+S+Manassas+St,+Memphis+TN+38163&entry=gmail&source=g University of Tennessee Health Science Center Office 901 448-7050 <(901)%20448-7050> CELL 901 604 4752 <(901)%20604-4752> Office: Translational Science Research Building, Room 407 EMAIL: rwilliams@uthsc.edu Alternative email: labwilliams@gmail.com SKYPE: robwwilliams

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pjotrp commented 6 years ago

Should be fixed now. Please test.