vcf-vcf intersect error

[PHemarajata]

Hi, I ran into this error during the ARTIC workflow:

index file localref.fa.fai not found, generating... /Users/peerahemarajata/galaxy/database/jobs_directory/000/137/tool_script.sh: line 25: 48088 Segmentation fault: 11 vcfintersect -v -r 'localref.fa' -w "0" -i '/Users/peerahemarajata/galaxy/database/objects/4/9/1/dataset_491da1b9-10f9-42a5-8d32-75c302cb6dc1.dat' '/Users/peerahemarajata/galaxy/database/objects/f/e/5/dataset_fe5536e9-af7c-4279-91eb-3afd1a196ef8.dat' > '/Users/peerahemarajata/galaxy/database/objects/0/0/6/dataset_00634612-08a3-4a35-bb49-0184a8e303a4.dat'

I looked at the command and there was no index file as an input for vcfintersect, only the reference FASTA which I have copied to the working history and specified as a reference input for a re-run, but I also ran into the same problem. Thank you!

[wm75]

The indexing should be done automatically for you. What's the source of your fasta file? Can you run NormalizeFasta from the Picard package over it?

[PHemarajata]

Did you mean to use the NormalizeFasta tool to process the FASTA to use as the initial input for the workflow? I can try that.

My FASTA was the one I downloaded from NCBI.

[PHemarajata]

Used FASTA processed with NormalizeFasta as input for the workflow (LINE_LENGTH; default=100, TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False) and still the same error.....

index file localref.fa.fai not found, generating... /Users/peerahemarajata/galaxy/database/jobs_directory/000/157/tool_script.sh: line 25: 50386 Segmentation fault: 11 vcfintersect -v -r 'localref.fa' -w "0" -i '/Users/peerahemarajata/galaxy/database/objects/8/9/f/dataset_89ff652d-83a3-48fb-9208-0690b2817e80.dat' '/Users/peerahemarajata/galaxy/database/objects/e/a/7/dataset_ea7985dc-b951-4955-b3ef-955370e1f419.dat' > '/Users/peerahemarajata/galaxy/database/objects/0/2/a/dataset_02aad5ff-2530-488a-8857-a69947e19ccc.dat'

[PHemarajata]

BTW I am running this workflow on a local Galaxy instance on MacOS Catalina.

[PHemarajata]

I have come to a conclusion that this is a MacOS problem, since there was absolutely no issue when I had the workflow running on a Galaxy instance on a native Ubuntu or the official Docker container which is Ubuntu. I had to switch to trying Galaxy on a MacOS since my new MB Pro does not play well with Ubuntu. Is there a way to make this work with Mac? Maybe I should be asking this on the Galaxy forum.......