STAR mapper: unrecoginzed parameter name "sjdbInsertSave" in input "genomeParameters.txt

Question

[diarmaidtobin]

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

[iraun]

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.

[diarmaidtobin]

You're right, sorry!

Answer 1

[diarmaidtobin]

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

Answer 2

[erwan.scaon]

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 ?

[erwan.scaon]

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.