Hello I try to use sortmerna 1st step (indexdb_rna..... ok with one or multiple ref) 2d step (usiing the data in sotmerna-2.1b directory as a example, idem with another file.fastq or file.fasta) my working directory is sotmerna-2.1b/
time sortmerna --ref rRNA_databases/silva-bac-16s-id90.fasta,index/silva-bac-16s-db --reads tests/data/illumina_GQ099317.fasta --sam --num_alignments 1 --fastx --aligned test_rRNA --other test_non_rRNA -v (without --log, option not recognized)
result:
File [rRNA_databases/silva-bac-16s-id90.fasta,index/silva-bac-16s-db] appears to be a relative path. Trying to locate in current directory and in the working directory ...File [rRNA_databases/silva-bac-16s-id90.fasta,index/silva-bac-16s-db] has not been found in the current directory. Trying the working directory ...[opt_ref:195] Could not locate File [rRNA_databases/silva-bac-16s-id90.fasta,index/silva-bac-16s-db] neither at current path ["/home/cdecraene/sortmerna_db/sortmerna-2.1b"] nor in Workdir [""]
ERROR: Reference file (FASTA) absolute or relative path. Use mutliple times, once per a reference file
Please, edit your post to make it clear and use the insert code button to highlight the code. As it is it is quite hard to read the code from the text.
From the error message it seems that you have a problem with the paths that you're providing. Perhaps giving absolute file/folder paths will make it easier for you and it'll solve the problem: https://www.computerhope.com/issues/ch001708.htm
António