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GuoliangLi-HZAU / BatMeth2

BS-seq analysis pipeline
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core dumped of BatMeth2 #3

Open chhylp123 opened 5 years ago

chhylp123 commented 5 years ago

I have ran BatMeth2 align by the following commands: ''' ./BatMeth2 align -g Homo_sapiens.GRCh38.dna.primary_assembly.fa -1 ../../../ssd/SRR5453774_1_val_1.fq -2 ../../../ssd/SRR5453774_2_val_2.fq -o SRR5453774.bam -p 28 '''

it reported: ''' ++++++++++++++++++++++penguin: penguin.cpp:5530: void Print_Pair(std::priority_queue<Alignment_Pair, std::vector, Comp_Align_Pair>&, Hit_Info&, Hit_Info&, char, char, READ&, READ&, unsigned char, char, char, FILE, Final_Hit&, Final_Hit&, READ&, READ&, MEMX&, MEMX&, BWT, BWT): Assertion `T.Loc!=INT_MAX' failed. /home/nhpcc502/chhy/BatMeth2-master/bin/batmeth2-align: line 36: 87197 Aborted (core dumped) $DIR/penguin $CMDLINE ''' could you help me to solve this problem? Thank you very much.

GuoliangLi-HZAU commented 5 years ago

We have fixed the problem you mentioned, please download the latest version to run. If you have any questions, please contact us. Thank you for your question.

chhylp123 commented 5 years ago

We have fixed the problem you mentioned, please download the latest version to run. If you have any questions, please contact us. Thank you for your question.

Thanks very much. May I ask should I rebuild index?

GuoliangLi-HZAU commented 5 years ago

No need to rebuild the genome index. Thanks.

chhylp123 commented 5 years ago

I have another problem about the output of BatMeth2. It seems all of the alignment results are written to the output SAM file. May I ask which types of alignment are available? I mean how can I select the unique best alignment? Thank you in advance.