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ZhouQiangwei / dmtools

BS-seq, WGBS, NOMe-Seq, RRBS data storage and analysis tool
https://dmtools-docs.rtfd.io
MIT License
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Core dump in dmtools-0.1.8 after processing chroms #3

Open enzeas opened 8 months ago

enzeas commented 8 months ago

After processing all chromosomes, the bam2dm tool in version 0.1.8 of dmtools is causing a memory leak and resulting in a core dump. The logs indicate the following:

[DM::calmeth] Free mem in Methy_List [DM::calmeth] Free mem in chromsUse [DM::calmeth] Free mem in all others

Error in `/datd/software/GitHub/dmtools-0.1.8/bam2dm': free(): invalid pointer: 0x0000000105096130 ======= Backtrace: ========= /usr/lib64/libc.so.6(+0x81329)[0x2ba72083d329] /datd/software/GitHub/dmtools-0.1.8/bam2dm[0x405061] /datd/software/GitHub/dmtools-0.1.8/bam2dm[0x406a16] /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ba7207de555] /datd/software/GitHub/dmtools-0.1.8/bam2dm[0x407438] ======= Memory map: ======== 00400000-004c1000 r-xp 00000000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm 006c0000-006c1000 r--p 000c0000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm 006c1000-006c2000 rw-p 000c1000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm

Environment: Operating System: Linux mgt 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 GNU/Linux dmtools Version: 0.1.8 GNU Make 4.3 g++ (GCC) 11.1.0

If it would facilitate the resolution process, I am available on WeChat for further discussion.

ZhouQiangwei commented 8 months ago

Hi, This is the final memory release. I just tested my system, and there is no issue on my end. I will further test on a different system. Additionally, you can use "dmtools viewheader -i file.dm" to check if the file is corrupted. If the file is normal, you can ignore this issue.

enzeas commented 8 months ago

viewheader seems to work normal, but view dit not work. ./dmtools viewheader -i N503.dm Ver code: 32768 BM_END: no BM_COVER: no BM_CONTEXT: no BM_STRAND: no BM_ID: no Levels: 0 indexOffset: 0x0 bufSize: 0 extensionOffset: 0x0 nBasesCovered: 0 sumData: 0.000000 minVal: 0.000000 maxVal: 0.000000 Chromosome List idx Chrom Length (bases) 0 GRCh38_chr1 248956422 1 GRCh38_chr2 242193529 .......

./dmtools view -i N503.dm [Mode] ------------- View all meth Done and free mem

ZhouQiangwei commented 8 months ago

Please provide the command of 'dmtools bam2dm', thanks

ZhouQiangwei commented 8 months ago

Hi, In the GCC 11.1.0 environment, I encountered errors while installing htslib. Previously, I tested it in the GCC 4.8.5 environment. If possible, you can use Conda to create an environment with GCC 4.8.5 and reinstall dmtools to complete the analysis.

enzeas commented 8 months ago

Hi, zhou,

I've recently rebuilt dmtools and encountered an issue while running the following command: ./bam2dm -g /datf/mapping_db/bis_db/bismark_index_GRCh38_GRCm38_lambda_pUC19/GRCh38_GRCm38_lambda_pUC19.fa -i /datd/data/Methy/20231128_singlecell/N503.bam -o N503.dm

Here's the tail of the error log: [DM::calmeth] loaded and store chrL 49195 261 [DM::calmeth] loaded and store pUC19 2686 262 [DM::calmeth] len count GCcount 5830674373 263 2310436966 [DM::calmeth] Longest chr: 248956422 [DM::calmeth] Processing 1 out of 1. File: /datd/data/Methy/20231128_singlecell/N503.bam, 0 Floating point exception (core dumped)

Environment: Operating System: Linux mgt 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 GNU/Linux dmtools Version: 0.1.8 GNU Make 4.3 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

Thank you for your assistance.

ZhouQiangwei commented 5 months ago

This may be an issue with different environmental versions. I will adapt it to conda installation as soon as possible. Thank you.