bschilder
commented
2 years ago Ah, sorry about that, that was a single-letter typo in my tryCatch wrapper. Just pushed a fix.
Closed AMCalejandro closed 2 years ago
bschilder
commented
2 years ago Ah, sorry about that, that was a single-letter typo in my tryCatch wrapper. Just pushed a fix.
bschilder
commented
2 years ago Also, just a note I found easier to track bugs in the previous version, as the messager told you the exact script the workflow was falling in. Now, I find challenging knowing where the issue is as there are many scripts and I do not know the exact workflow So, based on the output I paste below, I tracked the workflow until query_vcf.R. Then, I get lost. If you have any suggestion to make debugging easier or any draft showing the workflow within each echoverse package, that would be great.
This is a good point, there's so many steps that debugging does become very tricky. trackBack is normally helpful but because I have the tryCatch wrapper for locus (finemap_locus) traceback is not enabled. It might be time to remove the tryCatch (or at least make it an option) to enable better bug tracing.
Regarding the scripts, you mean output like this?
( grep ^'SNP' .../nalls2019.fullSS_subset.tsv; grep
-v ^'SNP' .../nalls2019.fullSS_subset.tsv | sort
-k2,2n
-k3,3n ) > .../file8ed6728213b_sorted.tsvThis abbreviated printing is done by echoconda::cmd_print, which I made to try and declutter the output messages. But if you think it does not harm than good I can change the default back to using full paths. Might do this by making verbose have more options than just T/F (0,1,2) to control the verbosity level.
AMCalejandro
commented
2 years ago Not sure we are talking about the same thinf, but yeah, that could be useful as well.
I was just referring to this previous kind of printing (Example)
[1] "LD:: Standardizing summary statistics subset."
[1] "++ Preparing Gene col"
[1] "++ Preparing A1,A1 cols"
[1] "++ Preparing MAF,Freq cols"
[1] "++ Inferring MAF from frequency column..."
[1] "++ Preparing N_cases,N_controls cols"
[1] "++ Preparing `proportion_cases` col"
[1] "++ 'proportion_cases' not included in data subset."
[1] "++ Preparing N col"
[1] "+ Preparing sample_size (N) column"
[1] "++ Using `sample_size = 3572` TRUE"
[1] "++ Preparing t-stat col"
[1] "+ Calculating t-statistic from Effect and StdErr..."
[1] "++ Assigning lead SNP"
[1] "++ Ensuring Effect, StdErr, P are numeric"
[1] "++ Ensuring 1 SNP per row"
[1] "++ Removing extra whitespace"
[1] "++ Saving subset ==> /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/EARLY_PD/POST_GWAS/ECHOLOCATOR/RESULTS/mixedmodels_GWAS/earlymotorPD_axial/MAD1L1/MAD1L1_earlymotorPD_axial_subset.tsv.gz"
[1] "LD:: Using UK Biobank LD reference panel."This way, I always found easy to find where something was going wrong in less than 10-15 minutes without being familiar how echolocatoR works
bschilder
commented
2 years ago Ok I'll keep that in mind as well. Opened a separate Issue to improve the messages: #105
1. Bug description
The simple pipeline does not work. I fall in the following error:
Also, just a note I found easier to track bugs in the previous version, as the messager told you the exact script the workflow was falling in. Now, I find challenging knowing where the issue is as there are many scripts and I do not know the exact workflow So, based on the output I paste below, I tracked the workflow until query_vcf.R. Then, I get lost. If you have any suggestion to make debugging easier or any draft showing the workflow within each echoverse package, that would be great.
2. Reproducible example
Code
Console output
Data
3. Session info
Thanks Brian!