bam2cgmap has been running Processing reads from chrM

[sunsong95]

Hi，thank you for such an excellent software.

After using bismark to deduplicate bam, I used samtools to sort, and when bam2cgmap bam files of different samples, the following problems occurred.

one of the samples：
bam2cgmap has been running Processing reads from chrM，no data in ATCGmap.gz/CGmap.gz/wig.gz. This is the log：

# input bam file: /home/myname/project/meththree/04.snv/Lib1_R1_001.umi_val_1_bismark_bt2_pe.deduplicated.sorted.bam
# source genome file: /home/myname/ref/human/ucsc.hg19.fasta
# [selected mode] Remove overlap
# prefix for output CGmap: /home/myname/project/meththree/04.snv/1
# Processing reads from: chrM

another sample
Although bam2cgmap is running normally, the log file has the following error at the end：
munmap_chunk(): invalid pointer

The above two bam files have the same processing flow, and the size of the two bam files is basically the same.
Is there any solution please?

[guoweilong]

Thanks for using CGmapTools. It is not recommended to direct call SNP using `cgmaptools bam2cgmap` (please refer to the HELP information for this command). You may using the Bismark's tool to call methylation, and use `cgmaptools bismark2cgmap` for converting the format. And `cgmaptools bam2cgmap` works well with the BAM files generated by BS-Seeker2. For the error message, you may try to avoid `--rm-Overlap` parameter when running `cgmaptools bam2cgmap`. Best, Weilong At 2022-07-05 09:04:02, "Neon" ***@***.***> wrote: Hi，thank you for such an excellent software. After using bismark to deduplicate bam, I used samtools to sort, and when bam2cgmap bam files of different samples, the following problems occurred. one of the samples： bam2cgmap has been running Processing reads from chrM，no data in ATCGmap.gz/CGmap.gz/wig.gz. This is the log： # input bam file: /home/myname/project/meththree/04.snv/Lib1_R1_001.umi_val_1_bismark_bt2_pe.deduplicated.sorted.bam # source genome file: /home/myname/ref/human/ucsc.hg19.fasta # [selected mode] Remove overlap # prefix for output CGmap: /home/myname/project/meththree/04.snv/1 # Processing reads from: chrM another sample Although bam2cgmap is running normally, the log file has the following error at the end： munmap_chunk(): invalid pointer The above two bam files have the same processing flow, and the size of the two bam files is basically the same. Is there any solution please? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[sunsong95]

Thanks for your answer,

I looked at the input requirements of the documentation of cgmaptools bismark2cgmap, but I found that I only generated the input of CpG, without CHG and CHH, as shown below:

After I removed --rmOverlap, the program seemed to work fine, but I don't know if that makes sense. I would like to know after using bismark deduplicate_bismark to deduplicate the bam file, if I use bam2cgmap to convert, do I still need to add --rmOverlap?

I see quickstart write:
If it’s paired-end sequencing strategy, we recommend you add --rmOverlap to the above command to remove overlapped region of two mate reads avoiding twice consideration of the same DNA fragment.

Please forgive me that I don't quite understand the meaning of this sentence. I don't know if the bam after deduplication needs to be added --rmOverlap