Error in dip-c seg and intermediate files about dip-c

[tanlongzhi]

Hi Yuyang,

I'll take a look at your error as soon as possible.

For an example .3dg file, there's already a FTP link in README.md; but it's not showing up because GitHub doesn't support FTP links. Here I've pasted it below for your convenience:

ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3271nnn/GSM3271352/suppl/GSM3271352_gm12878_06.impute3.round4.clean.3dg.txt.gz

The corresponding GEO accession contains final files like this for all single cells, as well as all intermediate files starting from raw.con.gz. However, the two earliest files, aln.bam and phased.seg.gz haven't been provided because of their large size.

[tanlongzhi]

Your error seems to come from a discrepancy in chromosome naming between your genome file (chr1 in your hg19.fa) and the SNP file you used (1 in snps/NA12878.txt.gz). You must change one of them to match the other.

The importance of chromosome name matching has been mentioned in an earlier comment for this repo, and another comment for the companion repo hickit.

[bioyuyang]

Ok. I will change the file and be careful in the following steps. Thanks so much for the quick respsonse or I will continue to get stuck.

…

________________________________ 发件人: Longzhi Tan <[email protected]> 发送时间: 2018年11月28日 22:36:52 收件人: tanlongzhi/dip-c 抄送: bioyuyang; Author 主题: Re: [tanlongzhi/dip-c] Error in dip-c seg and intermediate files (#21) Your error seems to come from a discrepancy in chromosome naming between your genome file (chr1 in your hg19.fa) and the SNP file you used (1 in snps/NA12878.txt.gz). You must change one of them to match the other. The importance of chromosome name matching has been mentioned in an earlier comment<#13 (comment)> for this repo, and another comment<#13 (comment)> for the companion repo hickit. ― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#21 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AlwYGLknFwmfTroxry8QLKkSCdXQ5mlUks5uzp-EgaJpZM4Y3luD>.

[liubinnk1]

Hi Tan,

I run the dip-c seg command and got the issues:

The messages is as following:
Traceback (most recent call last):
File "/THL8/home/liubin/software/dip-c-master/dip-c", line 130, in
main()
File "/THL8/home/liubin/software/dip-c-master/dip-c", line 42, in main
return_value = seg.seg(sys.argv[1:])
File "/THL8/home/liubin/software/dip-c-master/seg.py", line 115, in seg
seg_data.clean()
File "/THL8/home/liubin/software/dip-c-master/classes.py", line 204, in clean
for name in self.reads.keys():
RuntimeError: dictionary changed size during iteration

[tanlongzhi]

Hi @liubinnk1, please see my reply to your identical question in the other thread.
Best,
Tan