你好，我在 RNAseq-workflow中

[peiyu1223]

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 ）

[ssyamoako]

Hello peiyu1223, i went to the analysis and i was able to overcome that.
i will help you here.

what you have to do is this below:
sortmernaREF=/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/rfam-5.8s-database-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/rfam-5s-database-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/rfam-5s-database-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-arc-16s-id95.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-arc-16s-id95:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-arc-23s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-arc-23s-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-bac-16s-id90.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-bac-16s-id90:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-bac-23s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-bac-23s-id98:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-euk-18s-id95.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-euk-18s-id95:
/home/waccbip/Desktop/new_workflow/sortmerna_db/rRNA_databases/silva-euk-28s-id98.fasta,/home/waccbip/Desktop/new_workflow/sortmerna_db/index/silva-euk-28s-id98

#then after you index your database like this:
indexdb_rna --ref $sortmernaREF

then you run the final part of it this way:
for i in *_trimmed.fq;do
sortmerna
--ref $sortmernaREF
--reads $i
--aligned /home/waccbip/Desktop/new_workflow/results/3_rRNA/aligned/${i%.fq}_aligned.fq
--other /home/waccbip/Desktop/new_workflow/results/3_rRNA/filtered/${i%.fq}_filtered.fq
--fastx
-a 8
-v;done

I hope you follow the steps and get it fixed.

[bioinfotec]

The indexdb_rna binary has been removed from version 4.0.