-
Notifications
You must be signed in to change notification settings - Fork 4
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
Error on Jucier Pre, exit status 57 #5
Comments
First off, this is unrelated to your issue, but if you're running it on a cluster, you'll need to set some additional options to tell nextflow to run the jobs on the cluster nodes instead of the head nodes. See here for more info: https://www.nextflow.io/docs/latest/executor.html Other than that, you appear to be running the pipeline correctly. The only step that failed is the step to make a heatmap that you can open in juicebox. However, the error message says that there were 0 reads in the input, so my guess is that the scaffolding didn't work either. So first, take a look at the assembly output and the stats related to it. Does it look like the scaffolding actually worked (e.g., is the N50 bigger after scaffolding than before)? If not, how many reads did you start out with vs. how many got aligned? You can look at all the intermediate files by going into the work directory and then the first few characters of the directory for that step are in the nextflow output — for example, the alignment step's work directory should start with Hope this helps! |
Hi Any help is appreciated. Best |
Hi, So, mapping my reads to my assembly using bwa (-5SP is the option for Hi-C data). I then marked duplicates in the .sam file using samblaster. Converted it to BAM, and filtered out secondary alignments and unmapped reads; then further sorting by coordinates/read names for downstream Hi-C analyses. |
Hello,
Thank you for developing this pipeline.
I run the pipeline on a linux HPC system with the following input using -profile conda:
And I receive the following error;
EDIT; I am new to Hi-C, and I did not prepare this data myself; am I misunderstanding any preprocessing steps I need to do with the HiC illumina data, or am I not understanding the code? Thank you
The text was updated successfully, but these errors were encountered: