HiC-Pro

[Oksana Kutova]

Hello. 

I an running the HiC-Pro on a cluster. 

After I modify the config.txt I run the pipeline and got:

Run HiC-Pro 3.1.0
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Thu Nov  2 09:27:07 PDT 2023
Bowtie2 alignment step1 ...
Logs: logs/Sample1/mapping_step1.log

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Thu Nov  2 09:27:09 PDT 2023
Bowtie2 alignment step2 ...
Logs: logs/Sample1/mapping_step2.log
Logs: logs/Sample1/mapping_step2.log

--------------------------------------------
Thu Nov  2 09:27:10 PDT 2023
Combine R1/R2 alignment files ...
Logs: logs/Sample1/mapping_combine.log
Logs: logs/Sample1/mapping_combine.log

--------------------------------------------
Thu Nov  2 09:27:11 PDT 2023
Mapping statistics for R1 and R2 tags ...
Logs: logs/Sample1/mapping_stats.log
Logs: logs/Sample1/mapping_stats.log

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Thu Nov  2 09:27:11 PDT 2023
Pairing of R1 and R2 tags ...
Logs: logs/Sample1/mergeSAM.log
Logs: logs/Sample1/mergeSAM.log

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Thu Nov  2 09:27:17 PDT 2023
Assign alignments to restriction fragments ...
Logs: logs/Sample1/mapped_2hic_fragments.log
Logs: logs/Sample1/mapped_2hic_fragments.log

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Thu Nov  2 09:27:20 PDT 2023
Merge chunks from the same sample ...
Logs: logs/Sample1/merge_valid_interactions.log

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Thu Nov  2 09:27:20 PDT 2023
Merge stat files per sample ...
Logs: logs/Sample1/merge_stats.log

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Thu Nov  2 09:27:20 PDT 2023
Run quality checks for all samples ...
Logs: logs/Sample1/make_Rplots.log
make: *** [/home/HiC-Pro_3.1.0/bin/../scripts//Makefile:181: hic_qc] Error 1

#############

make_Rplots.log

##########

##Quality checks - Mapping results ...
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.3.1/bin/R CMD BATCH --no-save --no-restore "--args picDir='hic_results/pic/Sample1' bwtDir='bowtie_results/bwt2/Sample1' sampleName='Sample1' r1tag='ERR_1.fastq' r2tag='ERR_2.fastq'" /home//HiC-Pro_3.1.0/scripts/plot_mapping_portion.R logs/Sample1/plot_mapping_portion.Rout

##########

plot_mapping_portion.Rout

###########

> ####################################
> ##
> ## plotMappingPortion.R
> ##
> ####################################
> ## Get Mapping stat files for all fastq files of a given sample
> allmapstat_r1 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*",r1tag,"[[:print:]]*\\.mapstat$"), full.names=TRUE)
> allmapstat_r2 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*",r2tag,"[[:print:]]*\\.mapstat$"), full.names=TRUE)
>
> #allmapstat_r1 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*ERR_1.fastq[[:print:]]*\\.mapstat$"), full.names=TRUE)
> #allmapstat_r2 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*ERR_2.fastq[[:print:]]*\\.mapstat$"), full.names=TRUE)
>
>
> #print(" --- Debug: Here we print ----")
> #print(paste("Debug: path= ", bwtDir))
> print(allmapstat_r1)
character(0)
> print(allmapstat_r2)
character(0)
>
> #print("Debug: pattern= ")
> #print(paste0("^[[:print:]]*",r1tag,"[[:print:]]*\\.mapstat$"))
>
> stopifnot(length(allmapstat_r1)>0 && length(allmapstat_r2)>0)
Error: length(allmapstat_r1) > 0 && length(allmapstat_r2) > 0 is not TRUE
Execution halted

Any idea why I have and how I can fix this error?

Thank you