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Zhang-lab / ATAC-seq_QC_analysis

Atac-seq QC matrix
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DAR error #5

Open AndyR2 opened 4 years ago

AndyR2 commented 4 years ago

QC pipeline ran to completion with two samples called "IRI" and "Sham". Trying DAR with following command.

singularity exec /home/[my-path]/ATAC_IAP_v1.1.simg bash /atac_seq/pipe_code/DOR_analysis.sh $1=IRI $2=Sham

Several packages load, but after loading package 'DelayedArray', getting the following error
Error in factor(c(rep(0, as.numeric(args[8])), rep(1, as.numeric(args[9]))), : invalid 'labels'; length 2 should be 1 or 0 Execution halted

Can you help, please. Don't know whether this is an error in the original command, or something else. Where can I look at these "args" 1-9?

ShaopengLiu1 commented 4 years ago

Hi Andy, sorry for the delay.

Please try to remove the $1 and $2 in your cmd: singularity exec /home/[my-path]/ATAC_IAP_v1.1.simg bash /atac_seq/pipe_code/DOR_analysis.sh IRI Sham

The positional parameter can't recognize "$1=IRI", it will become "=IRI" as input if your $1 doesn't refer to sth.

Good luck : )