twbattaglia / rnaseq-workflow Goto Github PK

sortmerna
--ref $sortmernaREF
--reads results/2_trimmed_output/SRR1374921_trimmed.fq.gz
--aligned results/3_rRNA/aligned/SRR1374921_aligned.fq.gz
--other results/3_rRNA/filtered/SRR1374921_filtered.fq.gz
--fastx
--log
-a 4
-v
when i run abover code. I don't konwn how to fix the error.

[opt_ref:195] ERROR: The file /home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-arc-16s-id95.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-arc-16s-id95:/home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-arc-23s-id98.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-arc-23s-id98:/home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-bac-16s-id90.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-bac-16s-id95:/home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-bac-23s-id98.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-bac-23s-id98:/home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-euk-18s-id95.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-euk-18s-id95:/home/liulei/RNAseq-workflow/sortmerna_db/rRNA_databases/silva-euk-28s-id98.fasta,/home/liulei/RNAseq-workflow/sortmerna_db/index/silva-euk-28s-id98 is not an existing/valid absolute or relative path
Reference file (FASTA) absolute or relative path.

Like this, human have a database and can do "biocLite("org.Hs.eg.db") ", but if a species do not have db form Bioconductor. How should I do ?
Thanks.

到Step 3. Removing rRNA Sequences with SortMeRNA
中Run SortMeRNA (~15min)
sortmerna
--ref $sortmernaREF
--reads results/2_trimmed_output/sample_trimmed.fq
--aligned results/3_rRNA/aligned/sample_aligned.fq
--other results/3_rRNA/filtered/sample_filtered.fq
--fastx
--log
-a 4
-v
出现问题，因为-a换成了-threads而log没有这个指令，之后我出现了这样的错误（There was a problem, because -a was replaced by -threads and the log did not have this instruction, and then I got such an error ）
[opt_ref:186] ERROR: Could not locate File [sortmerna_db/rRNA_databases/silva-arc-16s-id95.fasta,sortmerna_db/index/silva-arc-16s-id95:sortmerna_db/rRNA_databases/silva-arc-23s-id98.fasta,sortmerna_db/index/silva-arc-23s-id98:sortmerna_db/rRNA_databases/silva-bac-16s-id90.fasta,sortmerna_db/index/silva-bac-16s-id95:sortmerna_db/rRNA_databases/silva-bac-23s-id98.fasta,sortmerna_db/index/silva-bac-23s-id98:sortmerna_db/rRNA_databases/silva-euk-18s-id95.fasta,sortmerna_db/index/silva-euk-18s-id95:sortmerna_db/rRNA_databases/silva-euk-28s-id98.fasta,sortmerna_db/index/silva-euk-28s-id98] neither at current path ["/home/peiyu/new_workflow"] nor in Workdir [""]
Reference file (FASTA) absolute or relative path.

   Use mutliple times, once per a reference file

非常抱歉我不会解决，能请教您一下么（I'm very sorry I won't solve it, can I ask you something ）