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dfguan / purge_dups

haplotypic duplication identification tool
MIT License
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Minimap2 error #126

Closed r-poloni closed 1 year ago

r-poloni commented 1 year ago

Hi, there is an error that I cannot understand (and maybe even the programme don't). I am working on a cluster, so I installed purge_dups cloning from github and following the instructions to install purge_dups and runner. When executing the code for the pipeline it returns an unknown error. Thank you to anyone that could help me! Here is the command

#! /bin/bash
source /local/env/envpython-3.7.1.sh
python /purge_dups_2/purge_dups/scripts/run_purge_dups.py /qc_assembly/purge_dups/config.cyd_blanc.json /purge_dups_2/purge_dups/src C_perspectalis

And here the output:

calculate coverage and self-alignment Unknown option: K Unknown option: K Unknown option: R"select[mem>5000] rusage[mem Unknown option: R"select[mem>20000] rusage[mem Usage: Usage: bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode] [-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q Queue Name] [-W Time] [-x Exclusive] [-h] [script]

bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode]
[-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q
Queue Name] [-W Time] [-x Exclusive] [-h] [script]

command minimap2 -I 4G -x map-pb -t 12 /scratch/rpoloni/blanc_pacbio/qc_assembly/hifiasm.Cp_w_m_0.16_no_HiC.bp.p_ctg.gfa.fa m64244_230212_204118_bc1003_bc1003_hifi_reads.fastq.gz >hifiasm.Cp_w_m_0.16_no_HiC.bp.p_ctg.gfa/coverage/m64244_230212_204118_bc1003_bc1003_hifi_reads.fastq.paf failed, return code: 2 unkown error, please check error log command /scratch/rpoloni/env/purge_dups_2/purge_dups/src/split_fa /scratch/rpoloni/blanc_pacbio/qc_assembly/hifiasm.Cp_w_m_0.16_no_HiC.bp.p_ctg.gfa.fa > hifiasm.Cp_w_m_0.16_no_HiC.bp.p_ctg.gfa/split_aln/hifiasm.Cp_w_m_0.16_no_HiC.bp.p_ctg.gfa.split.fa failed, return code: 2 unkown error, please check error log purge duplicates

r-poloni commented 1 year ago

At the end I run the pipeline manually. Not a solution, but it works!

erika-r-moore commented 1 month ago

Hello! I am having this same error. Can you clarify on what you did to run the pipeline manually? Thanks!

r-poloni commented 1 month ago

Hi Erika. I just ran the steps one by one as indicated in the readme at the chapter "pipeline guide". This gives you control over the errors and, in my case, allows to load a minimap environment I have installed on the cluster. Hope it helps.