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vcf-vcf intersect error
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!
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?
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.
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'
BTW I am running this workflow on a local Galaxy instance on MacOS Catalina.
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.......