“rule largeinsert_ratio” step error

[lsw0825]

Hi, I have tried to use your circlehunter tool to run our ATAC data, but the output file in one of the steps “rule largeinsert_ratio” haven‘t come out without any useful error message. Could you please analyze possible reasons and tell me what to do？ Help would be appriciated!

[yangmqglobe]

From the screenshot you provided, I cannot determine the cause of the issue as the log does not provide any useful information, and even the end part indicates that the operation has been completed. I would suggest you check the log file for that step at samples/{prefix}/{gsm}/log/{gsm}_largeinsert_ratio.log, or use parameters such as -p -r to get more information. Copy and paste the whole log may be better than a screenshot, too.

[lsw0825]

Thanks for your reply. I check the log file for that step "test_R23401985_largeinsert_ratio.log". Here is the complete content： INFO @ Mon, 05 Jun 2023 22:07:45: Read and build bedGraph... INFO @ Mon, 05 Jun 2023 22:07:45: Modify bedGraph... INFO @ Mon, 05 Jun 2023 22:07:45: Write bedGraph of modified scores... INFO @ Mon, 05 Jun 2023 22:07:45: Finished 'multiply'! Please check '/gpfs/home/lifesci/luosongwen/softwares/circlehunter/workspace/samples/test_R/test_R23401985/largeinsert/test_R23401985_largeinsert_ratio.bdg'! The log file indicates that the operation has been completed. But the file “test_R23401985_largeinsert_ratio.bdg” havn’t come out yet. Could you please analyze possible reasons？

[yangmqglobe]

It seems like Slurm mistakenly thought that the MACS2 process did not exit properly, causing Snakemake to consider the output files generated by MACS2 as unreliable and delete them (as seen in your first screenshot). You can try running the workflow locally without using Snakemake's cluster mode.

[lsw0825]

OK. Thanks for your help！

[Amine-7788]

Hi [lsw0825],

Can you send me your hg38.blacklist.bed please ?

Thank you

[yangmqglobe]

That is downloaded from ENCODE.