I have fasta files concatenated after cleaned up with kneaddata and I would like to develop a phylogenetic tree based on known reference genomes. At first i started with phylophlan. here are my parameters:
phylophlan -i /work/mindgut/kraken2/fasta_files --genome_extension .fastq -d phylophlan --databases_folder /work/mindgut/Lewis_sp/phylophlan_tutorial/phylophlan_databases/ -t a --diversity low -f /work/mindgut/Lewis_sp/phylophlan_tutorial/config/supermatrix_aa.cfg --fast --nproc 16 -o phylophlan_output
it does not run and I get this error;
[e] Command ‘[’/home/mindgut/.conda/envs/mindgut1/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query-gencode’, ‘11’, ‘–query’, ‘phylophlan_output/tmp/clean_dna/Sp_F.fastq’, ‘–db’, ‘phylophlan_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘phylophlan_output/tmp/map_dna/Sp_F.b6o.bkp’]’ returned non-zero exit status 1.
[e] gene_markers_identification crashed
I tried to recreate config file and re-run it but the issue persists!
Thanks for your help,
Ezgi