-
Notifications
You must be signed in to change notification settings - Fork 143
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
MACS2 steps did not carried out #336
Comments
I have the same issue as the author of the reported bug. wook2014, did you find the solution? |
No, I run it in HPC and I don't have many permissions to debug it. I run it manually by different softwares myself later. but it still helps a lot, I don't need to set a lot of parameters in bwa and samtools to mapping. |
First, sorry for the late reply. |
I will close this issue now for lack of activity, if you have any further questions please feel free to re-open it. |
Description of the bug
I have run chipseq workflow and I can not find the MACS2 result. I have checked the log file and it seemed that the steps after deeptools did not executed.
Command used and terminal output
nextflow run ~/chipseq/nf-core-chipseq-2.0.0/workflow/ -profile singularity --input ~/chipseq/data/chipseq.csv --outdir ~/chipseq/res --fasta ~/GRCh38/GRCh38_genomic.fna --gff ~/GRCh38/GRCh38_genomic.gff --bowtie2_index ~/GRCh38/bowtie2 --gtf ~/GRCh38/GRCh38_genomic.gtf --read_length 150 --macs_gsize 2875000000 --aligner bowtie2
Relevant files
nextflow.log
System information
Nextflow version ( 22.10.6 build 5843 )
Hardware ( HPC )
Executor ( pbs )
Container engine: ( Singularity )
OS ( Linux 3.10.0-862.el7.x86_64 )
Version of nf-core/chipseq ( 2.0.0)
The text was updated successfully, but these errors were encountered: