problem about methcounts

[shulil...@cau.edu.cn]

Hello！

     I can't get any results running methcounts for 5 days. my *.mr converted from bismark result, is about 136Gb. I also found methcounts takes zero memory and none error was reported. is there any thing wrong? here is my command.

/media/disk1/liusl/bin/methpipe-3.4.2/bin/methcounts -c /media/disk1/liusl/IGV_data/bosgenome/Bos_taurus.UMD3.1.fa -o ./methcounts/sperm1 Bos_sperm_1_sorted 

Bos_sperm_1_sorted is sorted as manual mentioned from *.mr

[Jianghan Qu]

I can't identify any problem in your command. 

Could you use -v option, and see if it reads in the chromosome file properly?

A message like "CHROMS_FOUND=25" should be printed once the chromosomes are identified.  

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Jenny

[Meng Zhou]

In addition to Jenny’s suggestion, can you try to split the genome file (Bos_taurus.UMD3.1.fa) to individual .fa files, with each representing one chromosome? I think you can avoid some performance issues by using separated .fa files.

Best regards,
Meng

[shulil...@cau.edu.cn]

It does not work either even I split the genome file to individual.fa files and -v option as you suggested, no error, no results for another four days running. should I wait for response?

[Andrew D. Smith]

If you run the program in verbose mode, there would never be a need to run it for 4 days. If you don’t see any messages printed to the screen after 10 minutes, likely there is a problem.

Please try and find a small example that reproduces this behavior. Try to select only reads that map to one of the chromosomes, and also use a file that only contains that chromosome. If this still produces the error, then cut the data set in half, and repeat. Hopefully you can make an example that reproduces the error and is small enough to send by email, in which case you can send the small example data set to the group and someone will figure out the problem.

Andrew

[shulil...@cau.edu.cn]

Thank you for your suggestion. But even I seperated the whole data into one chromosome each; problem still existed. accessory is my sorted mr files ,20000 rows from chr25. But  reference genome chr25,which is the smallest one, is too large to attach. So here is the download link online ftp://ftp.ensembl.org/pub/release-76/fasta/bos_taurus/dna/ 

my mr file is :

25      165     396     FRAG:ST-E00192:95:HF5VNCCXX:3:2224:9749:1959_1:N:0:     39      +       GAGTTCGGTTGTGGGTTGTGTGGTTTAAATATAGTATGTTTTTTGAAGAGAGGTGTGGTTCGTTGTTTTGATTTGTAGGTC

GGAGCGAAAGGGAGGCGAAGTGTAAGGTTGTTAGGGTGTTTCGCGTTAATCGTTTTTGTTTTCGGATATATTATTTTGAAGGTGTTTGATTTTATTTGTCTTTTGAAGTTAAGTAGGGTTTTGTTTGGTTAGTATTTTGGATGGGAGATT  AAFAFKKKKKKKKKKFKKFKKKKFK

KKKKKKKKKKKKKKKKKKKKKKKKKKKKAKFKKFKKKFFKKKKKKKKKKFKKKFKKKKKKKKFKKKKKKKKKKKKKAFKKFKKFKK,AFKKKKKKKFKKKFKFAFKKAKFKFFKKFKKKKKKKKFKFFFAFFFF<AKKFKKFFKKKKKKKKKKKFKKFAKKKKKKKKKKKKKKKKFK

KKKFKKKKKKKKKKKFKKKKKKKKFFFA<

25      177     429     FRAG:ST-E00144:112:HF5FJCCXX:8:2214:29897:15865_1:N:0:  38      +       GGGTTGTGCGGTTTAAATATAGTATGTTTTTTGAAGAGAGGTGTGGTTTGTTGTTTTGATTCGTAGGTTGGAGTGAAAGGG

AGGTGAAGTGTAAGGTTGTTAGGGTGTTTTGTGTTAATTGTTTTNGTTTTTGGATATATTATTTTGAAGGTGTTTNATTTTATTTGTTTTTTGAAGTTAAGTAGGGTTTTGTTTGGTTAGTATTTTGGATGGGAGATTATTTGGAAATTTTGGGTGTTGGAGGGCTTTTGT     A

AFFFKKKKKKFFFKKKKKKKKKKKKKKKKKKKKKKKKFKKFKFKKKFKKKKKKKKKKKKKKKKKKKKKKKKK<FKKKKKKKKK,AFFKKKAKKKKAKKAFKKKKFKA,FFKAKAAFKFAKKKKABKKKFKKAKFFFAFFKAAFKKKF<7AKFKKKBKKKKKKKKKKKKKKKKKKF7K

KKKKKKKKKKKKKKKKKFKKKFKKKKKKF,KKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKF,KKFFFAA

25      177     429     FRAG:ST-E00144:112:HF5FJCCXX:8:2214:29917:15830_1:N:0:  4       +       GGGTTGTGCGGTTTAAATATAGTATGTTTTTTGAAGAGAGGTGTGGTTTGTTGTTTTGATTCGTAGGTTGGAGTGAAAGGG

AGGTGAAGTGTAAGGTTGTTAGGGTGTTTTGTGTTAATTGTTTTNGTTTTTGGATATATTATTTTGAAGGTGTTTNATTTTATTTGTTTTTTGAAGTTAAGTAGGGTTTTGTTTGGTTAGTATTTTCGATGGGAGATTATTTGGAAATTTTGGGTGTTGGAGGTCTTTTGT     A

AFAFKKKKKKKKKKKKKKKKKKKKKFAKKKKKKKKKKKKK7F7FKFKKKKKKKKKKKKFFKKKKKKKKKKKKFKKKKKKKFKK,FFAKFK7FKKKAFKFKKKKKFKAFKKKKK,A,F7AKKKK<BFKF<7KAFKF<AFKFFKFFKKFA<A<7KKKBKKKKKKKKKKAKKKKFKKA7K

KAAKKFAF<KKKKKKKKFAKKKFKKKKKF<KF7KKKAKKKAKKKAKKKKKKKKKKKKFKKKKKKKFAFKFFFA,

25      187     400     FRAG:ST-E00192:96:HF5VHCCXX:7:1222:24507:43625_1:N:0:   42      -       AGGTGGTTTTTTATTTAAGATATTAATTAGGTAGGATTTTGTTTAGTTTTGGAGAGTAGATGAGATNGGGTGTTTTTAGGG

TGATATGTTCGGAGATAGAGGTGGTTGGTGCGGGGCGTTTTAATAGTTTTGCGTTTTGTTTTTTTTTTGTTTTGATTTGTAGGTTGGGATAATGGGTTGTATTTTTTTTTGGGGGGTGTGTTGTATTTGAGT    AAFFFKKKKKKKKKKKKAKKKKKKKKKKKKKFFKKKFKKKK

Can anyone help me to find what is the problem?

[Jianghan Qu]

I couldn't reproduce the error.  Output is attached.

$ ~/methpipe-3.4.2/bin/methcounts -c Bos_taurus.UMD3.1.dna.chromosome.25.fa Bos_sperm_1_chr25_20000 -v > test.meth
CHROMS_FOUND=1
PROCESSING:    25    (REQD MEM = 0.759GB)

I suspect that the methpipe program was not properly installed. Could you make a clean install of MethPipe, and see if there is any error during compiling?


​

 test.meth.bz2

​

[Di Wang]

Hi,

I have met the same problem with her.

methcounts runs for a long time but generate nothing in the output file.

my command is nohup /home/workspace/wangdi/softwares/methpipe-3.4.3/bin/methcounts -c /home/workspace/wangdi/WGBS/chrom_genome/ /home/workspace/wangdi/WGBS/8_sorted_start/SM.mr.sorted_start -v -o SM.meth &

Is there anyone could help me work this step out?

Many thanks.

Di

[Xiaojing Ji]

Hi Di,

It would be helpful if you can provide us the running information printed by methcounts with VERBOSE mode on. Also, we want to confirm that your reads were sorted with C locale (LC_ALL=C).

Thanks!

Liz

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Xiaojing Ji

Molecular and Computational Biology,

University of Southern California

1050 Childs Way, RRI 408c

Los Angeles, CA, 90089

[Di Wang]

Hi Xiaojing,

Thanks for your response. 

Is it must run with LC_ALL=C? 

As I understand LC_ALL=C is to set environmental variables, and when I was running with it, always report there is not such file or dir.  Thus I run the command without it. 

Thanks again. 

Di

Xiaojing Ji <xiao...@usc.edu> 于 2020年3月12日周四 下午9:40写道：

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