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GuoliangLi-HZAU / BatMeth2

BS-seq analysis pipeline
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batmeth2 calmeth basic_string::_M_construct null not valid #33

Open chgyi opened 2 years ago

chgyi commented 2 years ago

Hi , i run batmeth2 calmeth -g ref/hg38.fa -b chr1.sort.bam -m batmeth2.cal then get the error , bellow is the log

[2022:05:11 10:59:12] Processed 63013009 reads. [2022:05:11 10:59:19] Processed 64013011 reads. [2022:05:11 10:59:26] Processed 65013023 reads. [2022:05:11 10:59:33] Processed 66013025 reads. [2022:05:11 10:59:40] Processed 67013025 reads. terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid Aborted (core dumped)

chgyi commented 2 years ago

i have test other data , and get the same wrong . it happend in the last contig in ref genome。

ZhouQiangwei commented 2 years ago

hi,

could you please send us part of your alignment bam file which you thought coused this error. and we will test this and try to find the reason for this error.

mo

ZhouQiangwei commented 2 years ago

you can send the file to qwzhou@mail.hzau.edu.cn thanks

hengxing12 commented 2 years ago

yes, this process have errors.

Print output of NW_025316785.1

Print output of NW_025316786.1

Print output of NW_025316787.1

[2022:05:12 12:53:17] Processed 294074160 reads. Print output of NW_025316788.1

free(): double free detected in tcache 2 已放弃 (核心已转储)

ZhouQiangwei commented 2 years ago

Hi hengxing,

please let us know the input align file format is sam or bam format? and could you please check whether 'NW_025316788.1' is the last scaffold of your genome file.

mo

hengxing12 commented 2 years ago

yes, "bam " is input file.

the last one is NW_025316789.1, NW_025316788.1 may be finished.

Below is last output NW_025316788.1 3126145 + CHH 0 8 0.000000 null 0 0 U AGCAT NW_025316788.1 3126166 + CG 4 6 0.666667 null 0 0 Mh TGCGA NW_025316788.1 3126502 + CG 2 4 0.500000 null 0 0 H TGCGA NW_025316788.1 3126509 + CHH 0 6 0.000000 null 0 0 U AGCAA NW_025316788.1 3126527 + CHH 3 5 0.600000 null 0 0 M[hengxing@localhost AAP2]$

hengxing12 commented 2 years ago

HI Still seeing this error when updated the file.

[2022:05:12 16:51:35] Processed 293069037 reads. Print output of NW_025316785.1

Print output of NW_025316786.1

Print output of NW_025316787.1

[2022:05:12 16:51:40] Processed 294069857 reads. Print output of NW_025316788.1

free(): double free detected in tcache 2 已放弃 (核心已转储)

ZhouQiangwei commented 2 years ago

Hi, I think it may be due to the system environment. I modified some parameters of the software compilation process. Please try again.