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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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allmapstat_r1 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*",r1tag,"[[:print:]]*\\.mapstat$"), full.names=TRUE) #600

Open Oksanak22 opened 8 months ago

Oksanak22 commented 8 months ago

Hello.

I am running HiC-Pro on a cluster through: ./bin/HiC-Pro -i rawdata -o hic_results -c config-hicpro.txt -p

I got this error:

The following command will launch the parallel workflow through 1 torque jobs: sbatch HiCPro_step1_HIC.sh The following command will merge the processed data and run the remaining steps per sample: sbatch HiCPro_step2_HIC.sh (hic_pro_env) [ok@cedar5 HiC-Pro_3.1.0]$ cd hic_results/ (hic_pro_env) [o@cedar5 hic_results]$ sbatch HiCPro_step1_HIC_N.sh sbatch: error: NOTE: Your memory request of 12288M was likely submitted as 12G. Please note that Slurm interprets memory requests denominated in G as multiples of 1024M, not 1000M. sbatch: error: ---------------------------------------- sbatch: error: The specified partition does not exist, or the submitted job cannot fit in it... sbatch: error: Please specify a different partition, or simply submit the job without the --partition option, sbatch: error: the scheduler will redirect it to the most suitable partition automatically sbatch: error: ---------------------------------------- sbatch: error: Batch job submission failed: Unspecified error

But when I run ./bin/HiC-Pro -i rawdata -o hic_results -c config-hicpro.txt without "-p" option it runs to some points and after

Run quality checks for all samples ... Logs: logs/Sample1/make_Rplots.log make: *** [/project/6058390/pore-c-py/wf-pore-c/wf-pore-c/hic_pro_installed/HiC-Pro_3.1.0/bin/../scripts//Makefile:181: hic_qc] Error 1

And in make_Rplots.log I have

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

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)

print(allmapstat_r1) character(0) print(allmapstat_r2) character(0)

stopifnot(length(allmapstat_r1)>0 && length(allmapstat_r2)>0) Error: length(allmapstat_r1) > 0 && length(allmapstat_r2) > 0 is not TRUE Execution halted

Could you help me with that why do I keep getting this error? Thank you