methcounts -c error

[FIDES LAY]

Hi,

I am trying to run methcounts, but runs into the following error where it cannot find the genome fasta file:

methcounts -c ~/hg19/ -v -o OV10-S_sort_rmdup.mr.sort.meth OV10-S_sort_rmdup.mr.sort

CHROMS_FOUND=93

could not find chrom: (NULL)

The fasta file for each chromosome is in the directory specified by -c and was downloaded from UCSC, so I am not sure where this error is coming from. The input file was generated by running to-mr and sorted. I would appreciate any suggestion here. 

Thanks,

Fides

[Meng Zhou]

Can you check the first few lines of your input file OV10-S_sort_rmdup.mr.sort? This error is caused by a non-exist chromosome included in your mapped read file.

Best regards,
Meng

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[Fides Lay]

Thanks for the suggestion -- I found that the first ~80,000 lines were null --deleting these lines solved the problem with methcounts.

head OV10-S_sort_rmdup.mr.sort

(NULL) 0 0 X 0 +

(NULL) 0 0 X 0 +

(NULL) 0 0 X 0 +

(NULL) 0 0 X 0 +

Best regards,
Meng

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