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Old 10-22-2017, 01:11 AM   #641
Senior Member
Location: Cambridge, UK

Join Date: Sep 2009
Posts: 606

Hi Alan,

Thanks for making the files available. I have just tried to run your files with the following command line:

bismark2bedGraph --dir output_dir -o test --scaffold *G10G06*
And it finished just fine within a few minutes:

Created output directory output_dir/
Using these input files: CpG_OB_G10G06.sam.gz.txt CpG_OT_G10G06.sam.gz.txt

Summary of parameters for bismark2bedGraph conversion:
bedGraph output: test.gz
output directory: >/bi/home/fkrueger/Bismark_issues_3rd_parties/Alan_RRBS/output_dir/<
remove whitespaces: no
CX context: no (CpG context only, default)
No-header selected: no
Sorting method: Unix sort-based (smaller memory footprint, but slower)
Sort buffer size: 2G
Coverage threshold: 1
Methylation information will now be written into a bedGraph and coverage file

Using the following files as Input:
/bi/home/fkrueger/Bismark_issues_3rd_parties/Alan_RRBS/CpG_OB_G10G06.sam.gz.txt /bi/home/fkrueger/Bismark_issues_3rd_parties/Alan_RRBS/CpG_OT_G10G06.sam.gz.txt

Writing bedGraph to file: test.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: test.gz.bismark.cov.gz

Changed directory to /bi/home/fkrueger/Bismark_issues_3rd_parties/Alan_RRBS/output_dir/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file test.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OB_G10G06.sam.gz.txt to merged temp file
Finished writing methylation calls from CpG_OT_G10G06.sam.gz.txt to merged temp file
Sorting input file test.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file test.gz.methylation_calls.merged

Since the error message is actually:
sort: open failed: CpG_context_G08F07.txt: No such file or directory

Is there a possibility that you gave it the wrong file as input file by accident?
fkrueger is offline   Reply With Quote
Old 10-24-2017, 10:39 AM   #642
Location: Sheffield, UK

Join Date: Feb 2012
Posts: 15

Hi Felix,

I managed to get the script to work by having all the files (input, output) in the same directory as the bismark2Bedgraph script.

I could not find anything wrong with the file locations/file names that I had used previously but it works now!

Thanks again for your time and assistance
pig_raffles is offline   Reply With Quote

alignment, bisulfite, bisulphite, methylation, sequencing

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