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ChangLab / ATACPrimerTool

Primer design for ATAC-qPCR
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dim(X) must have a positive length #4

Closed yimi16 closed 4 years ago

yimi16 commented 4 years ago

Hi, I am trying to use APT to disign primer for my ATAC. It works well with test data but has some problems with my data. The information is shown below:

Rscript /root/Software/biosoft/ATACPrimerTool/scripts/find_qPCR_regions.R /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design/hela_atac_3/combined.o.coverage /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design/hela_atac_3/combined.f9.coverage 0.8 3 /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design/hela_atac_3/read_counts.txt /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design/hela_atac_3 /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design/hela_atac_3/APT_output/choosed1_peaks_qPCR_regions_corr0.8_cov3.bed (1895) INFO 12:17:38 | pypiper:manager:1134 > 

DEBU 12:17:38 | pypiper:manager:1131 > running
DEBU 12:17:38 | pypiper:manager:1131 > psutil.Popen(pid=1895, name='sh', status='sleeping', started='12:17:37')
DEBU 12:17:38 | pypiper:manager:1131 > running
DEBU 12:17:38 | pypiper:manager:1131 > psutil.Popen(pid=1895, name='sh', status='sleeping', started='12:17:37')
Error in apply(o.coverage.data[, 5:m], 1, function(x) x/t(lib.sizes.data)) :
dim(X) must have a positive length
Calls: t -> apply
Execution halted

The command i used is : python pipelines/ATACPrimerTool.py -O /mnt/g/data_analysis/analysis/hela-ATAC-primer/primer_design -S hela_atac_3 -G hg19 -I /mnt/g/data_analysis/analysis/hela-ATAC-primer/bams_1 -B /mnt/g/data_analysis/analysis/hela-ATAC-primer/choosed1_peaks.bed -fasta /mnt/g/genome_index/hg19_genome/hg19.fa

Any suggestions?

katieyost commented 4 years ago

Hi just wanted to check on this - did you resolve this issue?

yimi16 commented 4 years ago

Hi just wanted to check on this - did you resolve this issue?

Hi，i solved this problem several days ago so i closed this issue. Thanks for your concern.