Using 14 threads for the top and bottom strand indexing processes each, so using 28 cores in total
Writing bisulfite genomes out into a single MFA (multi FastA) file

Bisulfite Genome Indexer version v0.24.2 (last modified: 19 May 2022)

Step I - Prepare genome folders - completed



Step II - Genome bisulfite conversions - completed


Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer
Preparing indexing of CT converted genome in /gscratch/scrubbed/sr320/github/ceasmallr/data/genome/Bisulfite_Genome/CT_conversion/
Building a SMALL index
Preparing indexing of GA converted genome in /gscratch/scrubbed/sr320/github/ceasmallr/data/genome/Bisulfite_Genome/GA_conversion/
Building a SMALL index
Renaming BS_CT.3.bt2.tmp to BS_CT.3.bt2
Renaming BS_CT.4.bt2.tmp to BS_CT.4.bt2
Renaming BS_CT.1.bt2.tmp to BS_CT.1.bt2
Renaming BS_CT.2.bt2.tmp to BS_CT.2.bt2
Renaming BS_CT.rev.1.bt2.tmp to BS_CT.rev.1.bt2
Renaming BS_CT.rev.2.bt2.tmp to BS_CT.rev.2.bt2
Renaming BS_GA.3.bt2.tmp to BS_GA.3.bt2
Renaming BS_GA.4.bt2.tmp to BS_GA.4.bt2
Renaming BS_GA.1.bt2.tmp to BS_GA.1.bt2
Renaming BS_GA.2.bt2.tmp to BS_GA.2.bt2
Renaming BS_GA.rev.1.bt2.tmp to BS_GA.rev.1.bt2
Renaming BS_GA.rev.2.bt2.tmp to BS_GA.rev.2.bt2

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Parallel genome indexing complete. Enjoy!