Caution to users

[hsun3163]

This thread is dedicated to documenting potential problem user may encounter while using our the SOS based pipeline

[hsun3163]

1. Output target does not exist Error:
   Sometimes, when a run is completed, the following error, exemplified below, will occur, although the file is indeed there. This problem will resolve by simply rerunning the command with the -s build flag. This could be due to the SOS receiving a completion signal before generating the file. However, since rerunning the command will not produce the same error, the exact cause remains to be discovered.

ERROR: [VCF_QC (VCF_QC)]: [VCF_QC]: Output target output_rerun/data_preprocessing/genotype/DEJ_11898_B01_GRM_WGS_2017-05-15_21.recalibrated_variants.xqtl_protocol_data.add_chr.add_chr.leftnorm.filtered.bed does not exist after the completion of step VCF_QC