To the developer team,
Thank you again for your great contribution in this classifier.
I'm new to bioinformatic field and is working on nasopharyngeal microbiome.
I turned to Centrifuge because our previous analysis using MetaPhlAn2 had several output deemed as "100% unclassified" and we'd like to see if the whole-genome reference in Centrifuge could help us to find some clues.
I had successfully tried the index building and classification with provided examples,
but confronted with some download problem when i tried to build up an index for microbiome.
So firstly i tried the pre-built index according to the Quick Guide:
I used "nohup make p_compressed+h+v &"
however, the stdout log showed:
thus i retried "make p_compressed+h+v &", and find there was a "Download failed!" error:
[jennifer@localhost indices]$ Making: p_compressed+h+v: p_compressed+h+v
make -f Makefile IDX_NAME=p_compressed+h+v
make[1]: Entering directory /user/jennifer/JENNI/TOOLS/Centrifuge/centrifuge-1.0.4-beta/indices' [[ -d tmp_p_compressed+h+v ]] && rm -rf tmp_p_compressed+h+v; mkdir -p tmp_p_compressed+h+v Downloading and dust-masking viral centrifuge-download -o tmp_p_compressed+h+v -m -a "Any" -d "viral" -P 1 refseq > \ tmp_p_compressed+h+v/all-viral-any_level.map Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt ... Download failed! Have a look at valid domains at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq . make[1]: *** [reference-sequences/all-viral-any_level.fna] Error 1 make[1]: Leaving directory/user/jennifer/JENNI/TOOLS/Centrifuge/centrifuge-1.0.4-beta/indices'
make: *** [p_compressed+h+v] Error 2
so next, i tried to directly download refseq from ncbi according to your manual but same problem reoccurred:
Hence I checked the address
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq
using my own browser and found both archea & bacteria directory work well but viral directory is unable to open or read, thus i'd like to report this issue here to see if the hub do had problem as well if there's any solutions.
ypsung
commented
6 years ago
To the developer team, Thank you again for your great contribution in this classifier. I'm new to bioinformatic field and is working on nasopharyngeal microbiome. I turned to Centrifuge because our previous analysis using MetaPhlAn2 had several output deemed as "100% unclassified" and we'd like to see if the whole-genome reference in Centrifuge could help us to find some clues.
I had successfully tried the index building and classification with provided examples, but confronted with some download problem when i tried to build up an index for microbiome. So firstly i tried the pre-built index according to the Quick Guide: I used "nohup make p_compressed+h+v &" however, the stdout log showed:
thus i retried "make p_compressed+h+v &", and find there was a "Download failed!" error:
[jennifer@localhost indices]$ Making: p_compressed+h+v: p_compressed+h+v make -f Makefile IDX_NAME=p_compressed+h+v make[1]: Entering directory
/user/jennifer/JENNI/TOOLS/Centrifuge/centrifuge-1.0.4-beta/indices' [[ -d tmp_p_compressed+h+v ]] && rm -rf tmp_p_compressed+h+v; mkdir -p tmp_p_compressed+h+v Downloading and dust-masking viral centrifuge-download -o tmp_p_compressed+h+v -m -a "Any" -d "viral" -P 1 refseq > \ tmp_p_compressed+h+v/all-viral-any_level.map Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt ... Download failed! Have a look at valid domains at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq . make[1]: *** [reference-sequences/all-viral-any_level.fna] Error 1 make[1]: Leaving directory/user/jennifer/JENNI/TOOLS/Centrifuge/centrifuge-1.0.4-beta/indices' make: *** [p_compressed+h+v] Error 2so next, i tried to directly download refseq from ncbi according to your manual but same problem reoccurred:
Hence I checked the address ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq using my own browser and found both archea & bacteria directory work well but viral directory is unable to open or read, thus i'd like to report this issue here to see if the hub do had problem as well if there's any solutions.
Thank you again! Best regards, YP