diff --git a/TroubleShooting-&-FAQs.md b/TroubleShooting-&-FAQs.md index 0b7cc85..63b7ca9 100644 --- a/TroubleShooting-&-FAQs.md +++ b/TroubleShooting-&-FAQs.md @@ -3,22 +3,10 @@ ## Overview PhyloToL is not a commercial package, and so it is on each researcher to investigate errors. Here are a few starting points. * Be sure to have a ‘positive control’ for all files -* Check ALL error/log files -** Use commands like head or tail to quickly look at the PTL log files generated each time you submit a slurm job using sbatch -** Errors might originate at the beginning (head) that affect results downstream -** Usually the errors seen at the end of the run (tail) do no reflect where issues started; consult the Intermediate sub-folder in Output and/or other Katz lab members to track down the start of the issue -* Common errors: Incorrect file paths, incorrect file names, dependencies version in slurm/shell scripts +* Check ALL error/log files : Use commands like head or tail to quickly look at the PTL log files generated for each run. Also check the Intermediate sub-folder in Output to track down the issue +* Common errors: Incorrect file paths or names (capitalization and spacing matter), incorrect sequence names (search for 10 digit code throughout wiki), wrong dependencies version in slurm/shell scripts. - - - - - -## Common errors in setting up PhyloToL include: -* failure to name files or paths correctly (capitalization and spacing matter) -* failure to control names of sequences (search for 10 digit code throughout wiki) - # [FAQs](https://github.com/Katzlab/PhyloToL-6/wiki/TroubleShooting-&-FAQs#FAQs) ## Where can I find the figures and databases referred to here * Most items are found in our [figshare folder](https://figshare.com/account/home#/projects/196552)