Error Issue - Githubissues

123preksha commented 4 weeks ago

Hi nextflow run asadprodhan/sangerFlow -r f7e4fac --db=/mnt/d/ampliicon_analysis/ncbi-blast-2.15.0+ N E X T F L O W ~ version 0.30.1 Launching asadprodhan/sangerFlow [prickly_saha] - revision: f7e4fac2ac80d0137e6cbe7258cdb294a6058d41 ERROR ~ expecting '}', found ',' @ line 249, column 46. ery.baseName}_blast_sort.tsv"), emit: bl ^

1 error

-- Check '.nextflow.log' file for details

I am getting this error while running this command i tried to remove the syntax error but couldnt resolve the problem so please assist me with this.

asadprodhan commented 4 weeks ago

I will have a look at it at my earliest opportunity

-----

Dr Asad Prodhan

Laboratory Scientist

Department of Primary Industries and Regional Development

3 Baron-Hay Court, South Perth WA 6151

&

Adjunct Research Fellow

School of Biological Sciences

University of Western Australia

35 Stirling Hwy, Crawley WA 6009

On Thu, 20 Jun 2024 at 8:12 pm, 123preksha @.***> wrote:

Hi nextflow run asadprodhan/sangerFlow -r f7e4fac https://github.com/asadprodhan/sangerFlow/commit/f7e4fac2ac80d0137e6cbe7258cdb294a6058d41 --db=/mnt/d/ampliicon_analysis/ncbi-blast-2.15.0+ N E X T F L O W ~ version 0.30.1 Launching asadprodhan/sangerFlow [prickly_saha] - revision: f7e4fac https://github.com/asadprodhan/sangerFlow/commit/f7e4fac2ac80d0137e6cbe7258cdb294a6058d41 ERROR ~ expecting '}', found ',' @ line 249, column 46. ery.baseName}_blast_sort.tsv"), emit: bl ^

1 error

-- Check '.nextflow.log' file for details

I am getting this error while running this command i tried to remove the syntax error but couldnt resolve the problem so please assist me with this.

— Reply to this email directly, view it on GitHub https://github.com/asadprodhan/sangerFlow/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQXT2GIVZ4SHUMKMA7GPJ3ZILBL3AVCNFSM6AAAAABJT2QABKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM3DIMRYHA3TKNA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

asadprodhan commented 4 weeks ago

Where did you try to remove the syntax error? There is NO ERROR in the script and config file. To confirm, I have run it again and it worked fine with the supplied test data:

nextflow run asadprodhan/sangerFlow -r f7e4fac --db="/path/to/your/blastn_database"

Can you run sangerFlow with the test dataset and sample description file supplied in the sangerFlow GitHub page? Here is the link: https://github.com/asadprodhan/sangerFlow. Read it carefully.

It will help you narrow down the source of your error.

If you can run sangerFlow with the supplied test dataset but not with yours, then check the following items:

Complete Blastn database
Correct path for the Blastn database [how to check if the path is correct? cd to the path, if you see lots of file starting with nt.xxx.*, then the path is correct]
Fasta files with headers
Sample description file in tsv format with headers
Run dos2unix * to make sure all the files are in UNIX format

Let me know how you go.