Seeking assistance with the "bismark_methylation_extractor" command.

[dianzhiyong]

Dear Bismark author,

I am currently using Bismark for the analysis of bsseq data. The code I am using is as follows: "bismark_methylation_extractor --gzip --genome_folder $genomepath --no_overlap -o ./methylation --parallel 20 --scaffolds $bam". However, the program stops after giving the following output:

” Processed lines: 59500000 Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Finished processing child process. Exiting.. “

It seems that the analysis did not complete. Any assistance would be greatly appreciated. Best regards zhiyongdian

[FelixKrueger]

I believe you asked the script to spawn 20 processes, of which 19 are 'child' processes, and one is the parent. Typically, once all 19 child processes exited successfully (the parent process will wait for the children to finish) the parent process will tidy up and finish the process. It might very well have finished by now?

[dianzhiyong]

thanks doctor The analysis is not complete and no error messages are being displayed. now i demonstrate the code and the results show below ： $ ls methylation

CHG_context_H1.deduplicated.txt.gz CHH_context_H1.deduplicated.txt.gz CpG_context_H1.deduplicated.txt.gz H1.deduplicated_splitting_report.txt H1.deduplicated_splitting_report.txt.10 H1.deduplicated_splitting_report.txt.10.mbias H1.deduplicated_splitting_report.txt.12 H1.deduplicated_splitting_report.txt.12.mbias H1.deduplicated_splitting_report.txt.14 H1.deduplicated_splitting_report.txt.14.mbias H1.deduplicated_splitting_report.txt.4 H1.deduplicated_splitting_report.txt.4.mbias

############# $ tail nohup.out Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 59500000 Processed lines: 59500000 Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Finished processing child process. Exiting.. Processed lines: 60000000 Finished processing child process. Exiting..

There is no issue with the test data provided in the Bismark software package. What do you think is the issue?

[dianzhiyong]

the operating system is almallinux

[FelixKrueger]

Hmm, when you type top is the process still running? Maybe it got killed somehow? Can you scan the nohup file for other anomalies? I would probably just rerun in and try to reduce the number of parallel processes, to maybe 2 or 4 in the first instance?

[dianzhiyong]

ok, thank you. I will follow your advice and rerun it