FM index load error - Githubissues

elisabethgoldman commented 4 years ago

I am getting "FM index load error" when indexing with BatMeth2 build_index rrbs. Below is an excerpt from the stdout; it looks like the error occurs as the last step each time Index Builder for Batman runs. Can you advise on how to resolve this? Your help is appreciated.

Finished saving BWT.  Elapsed time = 0.31 s

Loading BWT...
Finished loading BWT.  Elapsed time = 0.39 s

Building SA value...
SA Value generated : 35450147
SA Value generated : 70900294
SA Value generated : 106350441
SA Value generated : 141800588
SA Value generated : 177250735
SA Value generated : 212700882
SA Value generated : 248151029
SA Value generated : 283601176
SA Value generated : 319051323
SA Value generated : 354501470
SA Value generated : 354501474
Finished building SA value.  Elapsed time = 468.15 s

Building cached SA index...
Finished building cached SA index.  Elapsed time = 2.14 s

Finished all tasks.  Total elapsed time = 1388.96 s

Maximum amount of memory allocated:  2285794912
Maximum amount of memory dispatched: 2284652980
Number of char   :  2836011784
Bit per char     :  6.44

Deleting auxilliary files...
FM index load error 
-= Index Builder for Batman =-
Building on /gscratch/csde/smacklab/genomes/batmeth2
Stripping Mmul_8.0.1_chroms_w_lambda.fa and filtering nucleotides...
Converting G->A
Creating FASTA file of Reverse of the Genome...
Creating FM index of reverse genome...

GuoliangLi-HZAU commented 4 years ago

Hi, Could you please provide the information of the genome used? thanks.

elisabethgoldman commented 4 years ago

We are using the rhesus macaque genome (mmul8) with only chromosomal contigs.

rmvpaeme commented 4 years ago

were you able to solve this? I'm having the same issue with GRCh37 as well.

elisabethgoldman commented 4 years ago

No; I ended up going back to Bismark (which has been quite reliable).

GuoliangLi-HZAU / BatMeth2

FM index load error #11