can't donwload viral library #221
Comments
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This appears to be due to the centrifuge-download script line 368: "cut -f "$TAXID_FIELD,$FTP_PATH_FIELD,$FTP_PATH_FIELD2" "$ASSEMBLY_SUMMARY_FILE" | ". I manually changed it to: "cut -f "$TAXID_FIELD,$FTP_PATH_FIELD" "$ASSEMBLY_SUMMARY_FILE" | ", and that solved the issue for me. Further up in that script it on line 305 the FTP_PATH_FIELD2 variable is defined with the following comment, "## Needed for wrongly formatted virus files - hopefully just a temporary fix." So I guess the viral "assembly_summary.txt" has been reformatted so this previously needed fix is no longer necessary. |
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I have updated a patch to handle this formatting issue. Thank you for identifying this @mperisin-lallemand ! |
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Possible that there is again the same problem? |
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I can't download viral sequences. Is it because my running version is outdated? The program ends at 100% progress but the library folder is empty. centrifuge-download -o library -d viral refseq > seqid2taxid.map |
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Could you please share the assembly_summary.txt file under library/viral in your download folder? |
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The file is almost 7 Mb. See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the columns in this file.#assembly_accession bioproject biosample wgs_master refseq_category taxid species_taxid organism_name infraspecific_name isolate version_status assembly_level release_type genome_rep seq_rel_date asm_name asm_submitter gbrs_paired_asm paired_asm_comp ftp_path excluded_from_refseq relation_to_type_material asm_not_live_date assembly_type group genome_size genome_size_ungapped gc_percent replicon_count scaffold_count contig_count annotation_provider annotation_name annotation_date total_gene_count protein_coding_gene_count non_coding_gene_count pubmed_id |
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How about the assembly_summary_filtered file? There are several issues in the downloaded file, like MajorFull should be "Major\tFull", but I'm not sure whether this is copy/paste error. How about use the option "-g wget" to use another method to download the file? |
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Assembly_summary_filtered looks like this: |
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Using wget produces the same result. Also, seqid2taxid.map is empty. |
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Can you share the whole assembly_summary_filtered.txt file? There might be some formatting issue when copy/paste here. |
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here are both files. |
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Your file looks correct to me. Could you please run command like "cut -f6,20,21 assembly_summary_filtered.txt | awk -F "\t" '{if ($2~/ftp/) print $1"\t"$2; if ($3~/ftp/) print $1"\t"$3}' | sed 's#([^/]*)$#\1/\1_genomic.fna.gz#' " to see whether there is strange output like na_genomic.fna.gz on your system? |
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Sorry, I can't figure out the sed call. It turns an error. |
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"genomic_fna" does not appear in the output of the cut | awk command |
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it might be the bash version thing. Would command like "cut -f6,20,21 assembly_summary_filtered.txt | awk -F "\t" '{if ($2~/ftp/) print $1"\t"$2; if ($3~/ftp/) print $1"\t"$3}' | sed 's/([^/]*)$/\1/\1_genomic.fna.gz/' " work? You need the sed command to duplicate the folder name of the FTP site and append the _genomic.fna.gz extension. |
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No luck. |
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appending "_genomic.fna.gz" to the ftp address and looking for the file returns a 404 error: |
Could you please add the "-e" or "-E" option to the sed command. The FTP linke to a file is: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/857/045/GCF_000857045.1_ViralProj15142/GCF_000857045.1_ViralProj15142_genomic.fna.gz , there is a repetition of folder name. |
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same result: cut -f6,20,21 assembly_summary_filtered.txt | awk -F "\t" '{if ($2~/ftp/) print $1"\t"$2; if ($3~/ftp/) print $1"\t"$3}' | sed -E 's/([^/]*)$/\1/\1_genomic.fna.gz/' |
Hi,
when using
centrifuge-download, I couldn't download the viral library, while archea and bacteria were OK.Any suggestion ?
I used the version 1.0.4, and I installed it using conda.
Thanks in advance.
Alex
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