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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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Error in mapping for v1.0.2.3 #23

Closed realzhang closed 3 years ago

realzhang commented 3 years ago

Dear chhylp123:

I installed BitMapperBS v1.0.2.3 via conda and successfully indexed hg38, but encountered error during mapping as following:

$bitmapperBS --search /pub/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BitMapperBS/genome.fa --seq1 ../sh_OE.trimmed.first10w.R1.fq --seq2 ../sh_OE.trimmed.first10w.R2.fq -t 1 --bam -o sh.bitm.bam
fileName[0]: /pub/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BitMapperBS/genome.fa
fileName[1]: /pub/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BitMapperBS/genome.index
Read qualities are encoded by Phred+33...
GapOpenPenalty: 5, GapExtensionPenalty: 3, MistMatchPenaltyMax: 6
MistMatchPenaltyMin: 2, N_Penalty: 1
 Read files are in FASTQ format...
Open /pub/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BitMapperBS/genome.fa.index sucessfully!
Start load hash table!
refGenLength = 3099973729 
Open /pub/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/BitMapperBS/genome.fa.index.bs.pac sucessfully!
shapline=1698406910
BWT has been loaded!
hash table has been loaded!
SA_length=1904980163
sparse_suffix_array_length=774993433
SA_flag_iterater=121092726
high_occ_table_length=189208
段错误(吐核)

Thanks for your help.

realzhang commented 3 years ago

Resolved. I re-complied bitmapperbs from source, with gcc/g++ v7.3.1 (devtoolset-7 in centos7), and this remind me that errors have occurred during the first compilation by gcc v4. before I compiled from source, the conda installed version errs as the above. Thanks and hope this helps.