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wtsi-hpag / Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
MIT License
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scaff10x still running after 22 days #26

Open olechnwin opened 1 year ago

olechnwin commented 1 year ago

Hi,

I am running scaff10x using the following command:

/opt/Scaff10X/src/scaff10x \
                -nodes 30 \
                -data input.dat \
                 scaffolds_FINAL.fasta scaffolds_FINAL_scaff10x.fasta"

Started running on August 31st and the last output is on August 31st. This is the last output:

[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 2150538 reads in 1615.708 CPU sec, 58.529 real sec

This is my input.dat

q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L001_R1_002.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L001_R2_002.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L002_R1_002.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L002_R2_002.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L003_R1_002.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L003_R2_002.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L004_R1_002.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S2_L004_R2_002.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L001_R1_001.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L001_R2_001.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L002_R1_001.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L002_R2_001.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L003_R1_001.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L003_R2_001.fastq
q1=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L004_R1_001.fastq
q2=/Data/A673_10x_and_WGS/A673_10x/A673_10x_fastq/A673_combined_S4_L004_R2_001.fastq

I am wondering if there is anything I should done differently. Thank you in advance for your help.