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biologger / speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
GNU General Public License v3.0
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Already in excludedassemblies #13

Closed lanying closed 3 years ago

lanying commented 3 years ago

18 Oct 2021 08:44:28: > Start searching primer for Lachnoanaerobaculum_saburreum 18 Oct 2021 08:44:28: Run: collect data(Lachnoanaerobaculum_saburreum) 18 Oct 2021 08:44:28: Run gunzip /primerdesign/Lachnoanaerobaculum_saburreum/genomic_fna/GCF_000185385.1_ASM18538v1_genomic.fna.gz 18 Oct 2021 08:44:28: Run gunzip /primerdesign/Lachnoanaerobaculum_saburreum/genomic_fna/GCF_000257705.1_EsaburreumF0468v1.0_genomic.fna.gz 18 Oct 2021 08:44:28: Run gunzip /primerdesign/Lachnoanaerobaculum_saburreum/genomic_fna/GCF_001552975.1_ASM155297v1_genomic.fna.gz 18 Oct 2021 08:44:28: Run: create_GI_list(Lachnoanaerobaculum_saburreum) 18 Oct 2021 08:44:28: Run: run_prokka(Lachnoanaerobaculum_saburreum) 18 Oct 2021 08:44:28: Removed /primerdesign/Lachnoanaerobaculum_saburreum/fna_files/GCF_000257705-1_EsaburreumF0468v1-0_20211018.fna 18 Oct 2021 08:44:28: Removed /primerdesign/Lachnoanaerobaculum_saburreum/fna_files/GCF_001552975-1_ASM155297v1_20211018.fna 18 Oct 2021 08:44:28: Removed /primerdesign/Lachnoanaerobaculum_saburreum/fna_files/GCF_000185385-1_ASM18538v1_20211018.fna 18 Oct 2021 08:44:28: GCF_000185385-1_ASM18538v1 annotation required 18 Oct 2021 08:44:28: Run prokka --kingdom Bacteria --outdir GCF_000185385-1_ASM18538v1_20211018 --genus Lachnoanaerobaculum --locustag GCF_000185385-1_ASM18538v1 --prefix GCF_000185385-1_ASM18538v1_20211018 --cpus 0 genomic_fna/GCF_000185385.1_ASM18538v1_genomic.fna.gz 18 Oct 2021 08:44:29: GCF_000257705-1_EsaburreumF0468v1-0 annotation required 18 Oct 2021 08:44:29: Run prokka --kingdom Bacteria --outdir GCF_000257705-1_EsaburreumF0468v1-0_20211018 --genus Lachnoanaerobaculum --locustag GCF_000257705-1_EsaburreumF0468v1-0 --prefix GCF_000257705-1_EsaburreumF0468v1-0_20211018 --cpus 0 genomic_fna/GCF_000257705.1_EsaburreumF0468v1.0_genomic.fna.gz 18 Oct 2021 08:44:29: GCF_001552975-1_ASM155297v1 annotation required 18 Oct 2021 08:44:29: Run prokka --kingdom Bacteria --outdir GCF_001552975-1_ASM155297v1_20211018 --genus Lachnoanaerobaculum --locustag GCF_001552975-1_ASM155297v1 --prefix GCF_001552975-1_ASM155297v1_20211018 --cpus 0 genomic_fna/GCF_001552975.1_ASM155297v1_genomic.fna.gz 18 Oct 2021 08:44:30: Already annotated: 18 Oct 2021 08:44:30: ['GCF_000185385v1'] 18 Oct 2021 08:44:30: > Already in excludedassemblies: 18 Oct 2021 08:44:30: ['GCF_000257705v1', 'GCF_001552975v1']

I‘d like to know the reason why ['GCF_000257705v1', 'GCF_001552975v1'] in excludedassemblies, Which log file should I look for?

biologger commented 3 years ago

A summary of the input quality control can be found in the Summary directory /primerdesign/Summary/Lachnoanaerobaculum_saburreum/Lachn_sabur_qc_sequences.csv

If you are sure that the genome assemblies are ok, then you could copy/move the directories back to the target directory, delete the excluded_list.txt file (will remove the warning: "already in excludedassemblies ") and start a new pipeline run with the --ignore_qc option.

$ cp -r /primerdesign/excludedassemblies/Lachnoanaerobaculum_saburreum/* /primerdesign/Lachnoanaerobaculum_saburreum/
$ rm /primerdesign/excludedassemblies/Lachnoanaerobaculum_saburreum/excluded_list.txt
$ speciesprimer.py -t Lachnoanaerobaculum_saburreum --ignore_qc
lanying commented 3 years ago

Very appreciated for answering my question in your busy time. According to your suggestion, my problem has been solved, thank you vey much!