error in evaluating the argument 'table' in selecting a method for function 'match': undefined columns selected

[Gemma-Zhang-326]

Hi, Firstly, thankful for developing this useful tools. I'm doing the differential Fithichip loops analysis. However it keeps throwing this error.

***** Computing overlap of merged loops with the FitHiChIP loop file index: 2  name: MacaqueH3K4me_FitHiChIP.interactions_FitHiC.bed for the chromosome : chrM ***** 
Matching on: B1, B2

 ----> number of master loops : 2  number of overlapping loops in input file : 2 Joining, by = c("B1", "B2")

 ***** Assigned contact count and q-values for the FitHiChIP loop file index: 2 for the chromosome : chrM ***** 

 Merging reference ChIP-seq coverage values: file number : 1  file name : ./H3K4mediffanalysis/Human_hichipbedgraph_Diff/scaled_ChIP_Coverage_HumanH3K4me.bed Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function 'match': undefined columns selected
Calls: FillFeatureValues -> match -> [ -> [.data.frame
In addition: Warning message:
In data.table::fread(InpTempChIPCoverageFile, header = F, sep = "\t",  :
  File './H3K4mediffanalysis/Human_hichipbedgraph_Diff/temp_CurrChr_InpChIPCoverageFile.bed' has size 0. Returning a NULL data.frame.
Execution halted

I have tried different parameters but nothing changed. Really need help! A reply would be appreciated!

Here is my code which is executed to do the differential analysis.

Rscript /gpfs/home/biosoft/FitHiChIP-master/Imp_Scripts/DiffAnalysisHiChIP.r \
 --AllLoopList HumanH3K4me_FitHiChIP.interactions_FitHiC.bed,MacaqueH3K4me_FitHiChIP.interactions_FitHiC.bed \
 --ChrSizeFile /gpfs/home/biosoft/HiC-Pro_3.1.0/HiC-Pro_3.1.0/annotation/T2T-CHM13.chrom.sizes \
 --ChIPAlignFileList HumanH3K4me_T2T_merge_TPM_normalized_HiChiP.bedgraph,MonkeyH3K4me_Mmul_10_merge_TPM_normalized_liftoverT2T.final.sort.bedGraph \
 --OutDir ./H3K4mediffanalysis/Human_hichipbedgraph_Diff \
 --FDRThr 0.01 --DiffFDRThr 0.1 --CategoryList HumanH3K4me,MacaqueH3K4me 1>log 2>&1

[Gemma-Zhang-326]

Hi, The analysis went well after I removed the chrM lines manually.

[ay-lab]

Hi @Gemma-Zhang-326 Thanks for letting us know. We'll keep a track of this issue regarding chromosome names and resolve it in the coming release.