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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Unable to get the QC Plots #350

Closed ancient-learner closed 3 years ago

ancient-learner commented 4 years ago

Hi I am using the following command to get the QC plots and I was not able to get that done

HiC-Pro -i ./HIC_COMPLETE_OUT2/hic_results/data/SAMPLE/ -o ./HIC_QC -c ./Hi-C_config -s quality_checks

My ./HIC_COMPLETE_OUT2/hic_results/data/SAMPLE/ contains 

Sample1_rep1_genome.bwt2pairs.SinglePairs
Sample1_rep1_genome.bwt2pairs.DEPairs
Sample1_rep1_genome.bwt2pairs.REPairs
Sample1_rep1_genome.bwt2pairs.SCPairs
Sample1_rep1_genome.bwt2pairs.DumpPairs
Sample1_rep1_genome.bwt2pairs.FiltPairs
Sample1_rep1_genome.bwt2pairs.RSstat
Sample1_rep1_genome.bwt2pairs_interaction.bam
Sample1_rep1_genome.bwt2pairs.validPairs
Sample1_rep2_genome.bwt2pairs.SinglePairs
Sample1_rep2_genome.bwt2pairs.DEPairs
Sample1_rep2_genome.bwt2pairs.REPairs
Sample1_rep2_genome.bwt2pairs.SCPairs
Sample1_rep2_genome.bwt2pairs.DumpPairs
Sample1_rep2_genome.bwt2pairs.FiltPairs
Sample1_rep2_genome.bwt2pairs.RSstat
Sample1_rep2_genome.bwt2pairs_interaction.bam
Sample1_rep2_genome.bwt2pairs.validPairs
Sample1_rep3_genome.bwt2pairs.SinglePairs
Sample1_rep3_genome.bwt2pairs.DEPairs
Sample1_rep3_genome.bwt2pairs.REPairs
Sample1_rep3_genome.bwt2pairs.SCPairs
Sample1_rep3_genome.bwt2pairs.DumpPairs
Sample1_rep3_genome.bwt2pairs.FiltPairs
Sample1_rep3_genome.bwt2pairs.RSstat
Sample1_rep3_genome.bwt2pairs_interaction.bam
Sample1_rep3_genome.bwt2pairs.validPairs
Sample1_rep4_genome.bwt2pairs.SinglePairs
Sample1_rep4_genome.bwt2pairs.DEPairs
Sample1_rep4_genome.bwt2pairs.REPairs
Sample1_rep4_genome.bwt2pairs.SCPairs
Sample1_rep4_genome.bwt2pairs.DumpPairs
Sample1_rep4_genome.bwt2pairs.FiltPairs
Sample1_rep4_genome.bwt2pairs.RSstat
Sample1_rep4_genome.bwt2pairs_interaction.bam
Sample1_rep4_genome.bwt2pairs.validPairs
Sample.allValidPairs

The log file just says

Run HiC-Pro 2.11.4
--------------------------------------------
Tue Aug 11 13:15:15 EDT 2020
Run quality checks for all samples ...

But there are no QC plots in the output folder except the log raw_data and tmp folders

nservant commented 4 years ago

Hi, Could you please have a look in the log (especially, the Rout files) and look for any error message ? Thx