hello,
When I try to run metaphlan2,I get the following error MD5 checksums do not correspond. How can I solve this problem.
Have you tried deleting all the files stored in the metaphlan_databases folder?
hi, I met the same problem, where did you download the MetaPhlAn_databases? I cannot open the link.
Hi @fbeghini , I am facing the similar issue for humann3 and was going through your suggestion. Can you please suggest me exactly where I should place --offline flag for metaphlan3:
humann --input ‘/scratch/galaxy/files/000/100/dataset_100608.dat’ -o output --threads 32 –metaphlan-options="-t rel_ab --bowtie2db /mnt/galaxyIndices/mpa_v30_chocophlan_201901 --nucleotide-database ‘/mnt/galaxyIndices/genomes/general_dbs/humann3/chocophlan’ --translated-alignment ‘diamond’ --protein-database ‘/mnt/galaxyIndices/genomes/general_dbs/humann2/protein/uniref50/uniref/’ --search-mode ‘uniref50’ --pathways ‘metacyc’ --annotation-gene-index 8 --evalue ‘1.0’ --threads “${GALAXY_SLOTS:-4}” --memory-use minimum --prescreen-threshold ‘0.01’ --translated-subject-coverage-threshold ‘50.0’ --translated-query-coverage-threshold ‘50.0’ --xipe ‘off’ --minpath ‘on’ --pick-frames ‘on’ --gap-fill ‘on’ --output-format ‘tsv’ --output-max-decimals ‘10’ --output-basename ‘humann3’ && sed -i ‘s/humann3_Abundance/REVERSE_T4A_R.fastqsanger/’ ./output/humann3_pathabundance.tsv && sed -i ‘s/humann3_Coverage/REVERSE_T4A_R.fastqsanger/’ ./output/humann3_pathcoverage.tsv && sed -i ‘s/humann3_Abundance-RPKs/REVERSE_T4A_R.fastqsanger/’ ./output/humann3_genefamilies.tsv