Sicer outputting No such File, warning and Directory

Question

[takamichael]

Hi I have been using sicer to see if I can get a better peak call on the H3k27me3. I converted my BAM files, which have already been aligned via BWA to bed file.

I used the line of code below the example given:

Example: /SICER-rb.sh ["InputDir"] ["bed file"] ["OutputDir"] ["species"] ["redundancy threshold"] ["window size (bp)"] ["fragment size"] ["effective genome fraction"] ["gap size (bp)"] ["E-value"]

My code (editted the file names to fit):

SICER-rb.sh MP2_input.bed MP2_H3K27me3.bed folder_1 hg19 1 200 150 .8 600 100

The code seems to run fine but it keeps outputting an error indicating that chromosomes can't be read. I keep getting lines that look like the ones below:

warning: chrY reads do not exist in MP2_input.bed/MP2_H3K27me3.bed
Warning: chr1 reads do not exist in /gpfs/gsfs4/users/bimas_ltg/Histone_ChIPseq_2016/scriptsMEM.cmd/MACS/SCICER/scicer_files/MP2_Merge_H3K27me3-1-removed.bed

Thank you for your help !

[GenoMax]

Do you get anything when you do grep chrY MP2_input.bed/MP2_H3K27me3.bed?

[takamichael]

if I do grep MP2_input.bed or grep MP2_H3k27me3 it works; however, the error also says that their is not such file for grep chrY MP2_input.bed/MP2_H3K27me3.bed

[GenoMax]

Since those two are warning's it may be fine to proceed. You don't have data for those two chromosomes in those two files.

[takamichael]

I would proceed but the files outputted are mostly blank.