Comments (7)
Chlamydiales is two ranks above chlamydia genus. Here is the flow:
Chlamydiales -> Chlamydiaceae -> Chlamydia trachomatis
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A suggestion for phylogeny:
we can collate all the de novo fasta files into one folder and then run ksnp from there. I am currently testing ksnp here
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- separate genome from plasmid
I think this is not a top priority for now. Unless you've done it already.
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@gokeson for extracting chlamydia reads, which taxonomic level should we use?
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=813
Chlamydiota
Chlamydiia
Chlamydiales
Chlamydiaceae
Chlamydia/Chlamydophila group
Chlamydia
I usually select a rank a few levels above species to make sure we capture as many isolate reads as possible.
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some quick fixes:
rule index:
prefix = "resources/ctReferences"
#from "ctReference" to "ctReferences"
scaffold.yaml
dependencies:
- ragtag
#from "rag-tag" to "ragtag"
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error:
RuleException in rule scrub in file /home/oolago2/assembly_pipeline/fullTest_Dec23/CtGAP_test/ctgap/workflow/rules/2-scrub.smk, line 1:
AttributeError: 'OutputFiles' object has no attribute 'r1tmp', when formatting the following:
scrubby scrub-reads -i {input.r1} {input.r2} -o {output.r1tmp} {output.r2tmp} --kraken-db {params.db} --kraken-taxa "Archaea Eukaryota Holozoa Nucletmycea" --min-len {params.minlen} --minimap2-index {params.human} --kraken-threads {threads} --workdir {params.workdir:q} 2> {log}
echo -e "
Scrubby Kraken Extract
" >> {log}
scrubby scrub-kraken -i {output.r1tmp} {output.r2tmp} -o {output.r1} {output.r2} --extract --kraken-taxa {params.kraken_taxa_extract} --kraken-reads {params.workdir}/0-standardDB.kraken --kraken-report {params.workdir}/0-standardDB.report --kraken-threads {threads} 2>> {log}
touch {output.status}
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error:
RuleException in rule scrub in file /home/oolago2/assembly_pipeline/fullTest_Dec23/CtGAP_test/ctgap/workflow/rules/2-scrub.smk, line 1: AttributeError: 'OutputFiles' object has no attribute 'r1tmp', when formatting the following:
scrubby scrub-reads -i {input.r1} {input.r2} -o {output.r1tmp} {output.r2tmp} --kraken-db {params.db} --kraken-taxa "Archaea Eukaryota Holozoa Nucletmycea" --min-len {params.minlen} --minimap2-index {params.human} --kraken-threads {threads} --workdir {params.workdir:q} 2> {log} echo -e "
Scrubby Kraken Extract " >> {log}
scrubby scrub-kraken -i {output.r1tmp} {output.r2tmp} -o {output.r1} {output.r2} --extract --kraken-taxa {params.kraken_taxa_extract} --kraken-reads {params.workdir}/0-standardDB.kraken --kraken-report {params.workdir}/0-standardDB.report --kraken-threads {threads} 2>> {log} touch {output.status}
this error persists:
RuleException in rule scrub in file /home/oolago2/assembly_pipeline/fullTest_Dec23/CtGAP_test/ctgap/workflow/rules/2-scrub.smk, line 1:
AttributeError: 'OutputFiles' object has no attribute 'r1tmp', when formatting the following:
scrubby scrub-reads -i {input.r1} {input.r2} -o {params.r1tmp} {params.r2tmp} --kraken-db {params.db} --kraken-taxa "Archaea Eukaryota Holozoa Nucletmycea" --min-len {params.minlen} --minimap2-index {params.human} --kraken-threads {threads} --workdir {params.workdir:q} 2> {log}
echo -e "
Scrubby Kraken Extract
" >> {log}
scrubby scrub-kraken -i {output.r1tmp} {output.r2tmp} -o {output.r1} {output.r2} --extract --kraken-taxa {params.kraken_taxa_extract} --kraken-reads {params.workdir}/0-standardDB.kraken --kraken-report {params.workdir}/0-standardDB.report --kraken-threads {threads} 2>> {log}
touch {output.status}
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Related Issues (16)
- Changes for v0.02 HOT 7
- to-do HOT 1
- How to handle plasmids? HOT 5
- some quick fixes: HOT 1
- error: HOT 1
- add phylogeny output HOT 8
- Scrubby updates HOT 7
- reference 'guided' consensus assembly
- create plurality consensus from 24 reference genomes HOT 1
- rename outputs to sample name
- add dnaapler to reorientate contigs HOT 1
- automate ref-denovo for specific reference strain
- Add snippy for SNP detection HOT 3
- Add QUASt HOT 3
- Scrubby/fastp order HOT 6
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