Error in (amed + 1):(bmed - 1) : result would be too long a vector

[LiyanJi-code]

Hi, when I run ReadDepth on WGBS data, the errors appeared:

Error in (amed + 1):(bmed - 1) : result would be too long a vector Calls: new ... binParams -> calcWindParams -> fdrRate -> dividePeaks Execution halted

How can I solve it ? Thanks in advances.

[chrisamiller]

You're going to have to provide more information, including the exact parameters and command that you ran the tool with.

[LiyanJi-code]

@chrisamiller Sorry, I made a mistook in param file. The problem has been solved now. But I still want to share my parameters and commands when I run ReadDepth using WGBS data. Hope you give helpful comments, thanks. -------------------------BEGIN---------------------------------- Step 1. C_to_T converted hs37d5.fa preparation, bismark_genome_preparation --path_to_bowtie /usr/local/opt/bowtie2-2.2.8/ --verbose hs37d5.fa

Step 2. To prepare the chr.map.gz and chr.dat.gz files sh runEachChr.sh # with bin size of 1000, read length of 150bp ps, I use bismark to align the chr.reads.fastq to C_to_T converted hs37d5.fa. Step3. To download the entrypoint file and modify the param file. Here is my param file: readLength 150 fdr 0.01 overDispersion 3 gcWindowSize 1000 percCNGain 0.05 percCNLoss 0.05 chunkSize 5e6 verbose TRUE Step 4. To prepare the bed files using filtered CpG sites from BSMAP results. And the input.bam for BSMAP was generated by bismark aligner. awk -F "\t" '{print $1"\t"$2"\t"$3}' chr.CpG.BSMAP.output > chr.bed Step 5. Run the ReadDepth.r in shell Rscript ReadDepth.r -----------------------------END------------------------------------------ All the values in fifth column of alts.dat file were below the loss threshold. These seem weird.

Thanks, Best regards.