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PRIMUS_output.log accidentally being deleted during pre-PRIMUS step #1

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jtb324 opened this issue Sep 13, 2024 · 1 comment · May be fixed by #2
Open

PRIMUS_output.log accidentally being deleted during pre-PRIMUS step #1

jtb324 opened this issue Sep 13, 2024 · 1 comment · May be fixed by #2
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bug Something isn't working

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@jtb324
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jtb324 commented Sep 13, 2024

Issue Summary:

When running the preprimus step of compadre, the log file generated by PRIMUS (named PRIMUS_output.log) seems to be getting accidentally deleted. This file was created almost immediately in the target output directory when i initially ran the command. After 16 hours of runtime though this file is no longer present. I am also receiving the follow messages in the stdout from the terminal:

Scalar value @_[1] better written as $_[1] at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 705.
Use of uninitialized value $ersa_model_output in string ne at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 726.
Use of uninitialized value $ersa_results in string ne at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 726.
out_dir: test_primus_redo_9_12_24/
Use of uninitialized value in -e at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 778.
Use of uninitialized value $ibd_estimates{"FILE"} in pattern match (m//) at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 789.
Use of uninitialized value $trait_order[0] in hash element at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 793.
Use of uninitialized value within %traits in pattern match (m//) at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 793.
Use of uninitialized value $LOG in string eq at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 109.
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 111.

FILES AND COLUMNS
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 381.
LOG FILE: test_primus_redo_9_12_24//PRIMUS_output.log
Data stem: ./merged_files/merged_common_snps_with_rsids_and_missingness_filter
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 386.
Dataset results dir: test_primus_redo_9_12_24/
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 391.
Age file: none
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 393.
Sex file: none
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 400.
Affection file: none
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 407.
Trait weighting:
print() on closed filehandle $LOG at /belowshare/vumcshare/data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/primus_kickoff7.pl line 412.

It seems like at somepoint in the primus_kickoff7.pl script the LOG file handle is closed. It appears that PRIMUS still completes successfully but I think it would be of benefit to users to have this file because it provides some higher level cohesive information that the individual plink logs that PRIMUS creates doesn't provide incase the preprimus step should fail for some reason.

How to replicate

I used the following command to run the pre-PRIMUS pipeline:

 perl -d:NYTProf /data100t1/home/grahame/projects/compadre/primus/PRIMUS_v1.9.0/bin/run_PRIMUS.pl --file ./merged_files/merged_common_snps_with_rsids_and_missingness_filter --genome --no_pca_plot -o test_primus_red
o_9_12_24/ --degree_rel_cutoff 3 --no_IMUS --no_PR
@jtb324 jtb324 added the bug Something isn't working label Sep 13, 2024
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jtb324 commented Sep 13, 2024

update:

The pre-primus step actually seems to create the log file if the output directory is already made. If the output directory is not made primus will make it but the log file seems to be created

@jtb324 jtb324 linked a pull request Sep 13, 2024 that will close this issue
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@jtb324 jtb324 linked a pull request Sep 13, 2024 that will close this issue
PRIMUS_output.log not always being created #2
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PRIMUS_output.log not always being created belowlab/compadre
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