Fix the bug of missing flags for some subject; New functions of parallel computing and some additional issues

[lxwgcool]

We do have 200 subjects generated in the steps of merge subject. However we only get 198 subjects be ran in the phase of BAM recalibration. This issue is caused by 2 samples were copied to backup folder, which is unexpected!

[lxwgcool]

New Function and Fix Bug: missing flags, multi-cores and some issues Details: 1: gatk_build_bam_for_single_name_v4.sh (1) Update samtools from 1.8 to 1.13 (2) Add multiple threads(8) feature to "samtools sort" (3) Add multiple threads(8) feature to "samtools view" (3) Add multiple threads(8) feature to "samtools merge"

2: step7b_take_incoming_bams.sh (1) Add multiple threads(8) feature to "samtools index" (2) Move all files in backup folder to the reformatted original folder *Solve the issue of missing flags for some BAM files (moved into unexpected folder the)

3: step8_sync_and_recalibrate_bam.sh (1) Remove the unnecessary info in log (2) Add multiple threads resourced requirement in sbatch

4: AutoFramework.py (1) Add the specific class to record the subject info defined in keytable

• same as the the data structure in MergeSubject.py (2) For MergeSubject and Recalibration, add a function to show the bad samples that miss the flag file. (3) Require multi threads resources for step 2 "ReconstructBAMDir".

5: Backup2S3.py, job.sh (1) Add the correct path to save the log files from SLURM

6: MergeSubject.py (1) Remove the unnecessary info in log: do not print vRG info (2) Require multi threads resources (8 cores)

[lxwgcool]

1: gatk_build_bam_for_single_name_v4.sh (1) Remoe the archive stuff (we do not need it) (2) Change the layout of the code.

2: recalibrate_bam.sh (1) Update samtools from 1.8 tp 1.13 (2) Add multiple threads(8) feature to "samtools sort" (3) Add multiple threads(8) feature to "samtools view" (3) Add multiple threads(8) feature to "samtools index"