Question: STAR mapper: unrecoginzed parameter name "sjdbInsertSave" in input "genomeParameters.txt
0
gravatar for diarmaidtobin
2.7 years ago by
diarmaidtobin0 wrote:

Hey guys, currently I am trying to use STAR and during the process following issue occured:

After building the genome index with following command:

$ STAR --runMode genomeGenerate --runThreadN <# cpus> --genomeDir <genome output="" directory=""> --genomeFastaFiles <#input Genome FASTA file>

I got a 'genomeParameters.txt' file with following content:

(....) sjdbInsertSave Basic

Now as I tried to execute the mapping step:

$ STAR --genomeDir <directory with="" the="" genome="" index=""> --runThreadN <# cpus> --readFilesIn <fastq file=""> --outFileNamePrefix <outputprefix>

I get following error message in my shell:

Jun 20 10:41:14 ..... Started STAR run EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "sjdbInsertSave" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

I am quite new to this whole environment and also after checking the manual I'm still stuck. The parameter 'sjdbInsertSave Basic' should be ok or not? If anybody has a solution or an idea for further research I'd be grateful!

Cheers

rna-seq alignment • 1.6k views
ADD COMMENTlink modified 19 months ago by erwan.scaon630 • written 2.7 years ago by diarmaidtobin0

Please, add a little formating to your question. Write the commands and output in separated lines in order to make the question more readable, and therefore the users could help you more easily.

ADD REPLYlink written 2.7 years ago by iraun3.5k

You're right, sorry!

ADD REPLYlink written 2.7 years ago by diarmaidtobin0
0
gravatar for diarmaidtobin
2.7 years ago by
diarmaidtobin0 wrote:

Hey guys, the actual problem was my fastq file I guess. After repeating the process with other input files everything worked fine. Thanks anyway!

ADD COMMENTlink written 2.7 years ago by diarmaidtobin0
0
gravatar for erwan.scaon
19 months ago by
erwan.scaon630
Limoges - CBRS - France
erwan.scaon630 wrote:

I stumbled across the same issue (STAR, version 2.5.2b).

Exactly the same error message (with the wrong spelling for unrecoginzed).

Thing is, "sjdbInsertSave" is an actual parameter name, I don't get why it would be "unrecognized" all of a sudden.

Any tips ?

ADD COMMENTlink written 19 months ago by erwan.scaon630

Ok, my bad, this "error" was due to "version conflict" : STAR genome index was built with version 2.5.2b but mapping was attempted on a different cluster with an older version. Mapping with version 2.5.2b works fine.

ADD REPLYlink written 19 months ago by erwan.scaon630
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