outPrefix.align.log.txt

hengxing12 commented 2 years ago

hi I run pipeline mode, and have some errors.

report2html did not output "statistic html"， outPrefix.align.log.txt did not be produced by alignment

cp: 无法获取'./outPrefix.log.txt' 的文件状态(stat): 没有那个文件或目录 File ./outPrefix.align.log.txt Cannot be opened ....

ZhouQiangwei commented 2 years ago

Hi, .align.log.txt file is generated by calmeth, could you please check does the calmeth step is correct.

hengxing12 commented 2 years ago

hI, Guoliang

calmeth output is error and not finished. This problem is here, https://github.com/GuoliangLi-HZAU/BatMeth2/issues/33

ZhouQiangwei commented 2 years ago

Hi, I saw the error is 'double free', there is only few lines about free memory in process bam file. I have comment out this part, and updated it to github. please download and rerun calmeth. please let us known if this error still occurs. mo

hengxing12 commented 2 years ago

Hi, now is sh: /data/bahengxing/tools/BatMeth2-master/bin/bmtools: 没有那个文件或目录 sh: /data/bahengxing/tools/BatMeth2-master/bin/bmtools: 没有那个文件或目录 sh: /data/bahengxing/tools/BatMeth2-master/bin/bmtools: 没有那个文件或目录 File ./AAP2.align.log.txt Cannot be opened ....

ZhouQiangwei commented 2 years ago

sorry, i have uploaded the wrong version of BatMeth2.cpp main program, i will fix it soon.

ZhouQiangwei commented 2 years ago

Hi, I am just uploaded the new version, please try it. sorry for this again

hengxing12 commented 2 years ago

try again and no change, still error.

ZhouQiangwei commented 2 years ago

Is there more process information than before?

---Original--- From: @.> Date: Thu, May 12, 2022 18:31 PM To: @.>; Cc: @.**@.>; Subject: Re: [GuoliangLi-HZAU/BatMeth2] outPrefix.align.log.txt (Issue #34)

try again and no change, still error.

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hengxing12 commented 2 years ago

[2022:05:12 19:01:00] Processed 294069857 reads. Print output of NW_025316788.1

close and free short mem close and free short mem free(): double free detected in tcache 2 已放弃 (核心已转储)

ZhouQiangwei commented 2 years ago

yes, i think the error is here, there is two times print of "close and free short mem". could you please send your command to me?

------------------ 原始邮件 ------------------ 发件人: "GuoliangLi-HZAU/BatMeth2" @.>; 发送时间: 2022年5月12日(星期四) 晚上7:04 @.>; @.**@.>; 主题: Re: [GuoliangLi-HZAU/BatMeth2] outPrefix.align.log.txt (Issue #34)

[2022:05:12 19:01:00] Processed 294069857 reads. Print output of NW_025316788.1

close and free short mem close and free short mem free(): double free detected in tcache 2 已放弃 (核心已转储)

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ZhouQiangwei commented 2 years ago

Hi, I have uploaded the new version. please run calmeth and check whether there is still more than one times of "close and free short mem".

------------------ 原始邮件 ------------------ 发件人: "GuoliangLi-HZAU/BatMeth2" @.>; 发送时间: 2022年5月12日(星期四) 晚上7:04 @.>; @.**@.>; 主题: Re: [GuoliangLi-HZAU/BatMeth2] outPrefix.align.log.txt (Issue #34)

[2022:05:12 19:01:00] Processed 294069857 reads. Print output of NW_025316788.1

close and free short mem close and free short mem free(): double free detected in tcache 2 已放弃 (核心已转储)

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hengxing12 commented 2 years ago

[2022:05:12 23:00:33] Processed 294069857 reads. Print output of NW_025316788.1

close and free short mem 段错误 (核心已转储)

hengxing12 commented 2 years ago

/data/bahengxing/tools/BatMeth2/bin/calmeth -g ../index/genomic.fna -b AAP2.sort.bam -m AAP2

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.

hengxing12 commented 2 years ago

HI

The simple test is currently successful, but i did not see ".align.log.txt" that will be used by report2html.

mC/(C+T) {260 / 6952} = 3.739931% mCG/(CG+TG) {220 / 312} = 70.512821% mCHG/(CHG+THG) {14 / 1648} = 0.849515% mCHH/(CHH+THH) {26 / 4992} = 0.520833% Done and release memory!

ZhouQiangwei commented 2 years ago

great, please add -as 1 parameter for print .align.log.txt

DharmaBums1991 commented 1 year ago

great, please add -as 1 parameter for print .align.log.txt Hi，the auto cmd has added this parameter,but I still encounter this error.

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GuoliangLi-HZAU / BatMeth2

outPrefix.align.log.txt #34

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