# SARS-CoV-2 ARCTIC V4 files **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** gtn-tutorial, workflow, queued-gray-datasets, fastqsanger, sars-cov-2, paused-jobs, iwc-workflows\ **Created:** [January 18, 2022, 1:12pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342 "2022-01-18T13:12:56Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [January 18, 2022, 1:12pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/1 "2022-01-18T13:12:56Z")
Good day, Are there ARCTIC v4 amplicon info and v4 bed files to use for SARS-CoV-2 analysis. We recently started using the ARCTIC V4 primers. I had to try running the sequence data using the V3 primer set and bed on the SARS-CoV-2 workflow but it doesn’t generate any info. ---
**Author:** ![gbbio](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gbbio/32/366_2.png) [@gbbio](https://help.galaxyproject.org/u/gbbio)\ **Post date:** [January 18, 2022, 1:18pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/2 "2022-01-18T13:18:34Z")
This maybe? > **[artic-ncov2019/primer\_schemes/nCoV-2019 at master · artic-network/artic-ncov2019](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019)** > > master/primer\_schemes/nCoV-2019 ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [January 19, 2022, 7:58am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/3 "2022-01-19T07:58:13Z")
Hi @Kathleen_Subramoney, we’ve updated our shared covid-19 resources history on [usegalaxy.eu](http://usegalaxy.eu) a while ago to include more primer schemes. [Galaxy | Europe | Published History | COVID-19 resources](https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources) has ARTIC v4 primers (and amplicon info) and others since then. Cheers, Wolfgang ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [January 19, 2022, 11:08am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/4 "2022-01-19T11:08:10Z")
Thank you Wolfgang 🙂 ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [January 19, 2022, 11:08am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/5 "2022-01-19T11:08:51Z")
Yes this looks like it. Thank you. ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [February 4, 2022, 1:36pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/6 "2022-02-04T13:36:39Z")
Hi Wolfgang, So I used the v4 arctic primers but when I ran the workflow on my fastq files the fasta file that was generated just comprised of N’s. I ran the same samples on genome detective and it works fine. I’m not sure what I am doing wrong because it worked well when needed to run the workflow using V3. ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [February 4, 2022, 2:07pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/7 "2022-02-04T14:07:56Z")
@Kathleen_Subramoney I guess I need a bit more details if you want me to debug this. All Ns in the consensus sequence means that along the way you lost all your genome coverage somehow and since it’s happening only with the new v4 primer scheme the ivar trim step sounds like a plausible candidate. Look for empty (or nearly empty) BAM datasets generated as part of the workflow. I’m afraid that’s all I can say without seeing how you invoked the workflow or even which workflow exactly. ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [February 7, 2022, 6:34am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/8 "2022-02-07T06:34:24Z")
Dear Wolfgang, I am using the workflows as per attachments. I can take screenshots of how I invoke the workflow if that will be more useful, let me know. The ivar trim step gives the following info: Found 198 primers in BED file No affected primer binding sites found! Found 198 primers in BED file Writing to removed\_reads.bam Number of references: 1 Reference Name: NC\_045512.2 Reference Length: 29903 Using Region: NC\_045512.2 Sorted By Coordinate Kind Regards Kathleen (Attachment Galaxy-Workflow-2)_COVID-19\_\_consensus\_construction_(imported\_from\_uploaded\_file).ga is missing) (Attachment Galaxy-Workflow-1)COVID-19\_\_variation\_analysis\_on\_ARTIC\_PE\_data\_(imported\_from\_uploaded\_file).ga is missing) (Attachment Galaxy-Workflow-3)_COVID-19\_\_variation\_analysis\_reporting_(imported\_from\_uploaded\_file).ga is missing) ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [February 7, 2022, 7:02am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/9 "2022-02-07T07:02:27Z")
Sorry my attachments were rejected. These are the names of the workflows I am using for COVID. Galaxy-Workflow-2)_COVID-19\_\_consensus\_construction_(imported\_from\_uploaded\_file).ga Galaxy-Workflow-1)COVID-19\_\_variation\_analysis\_on\_ARTIC\_PE\_data\_(imported\_from\_uploaded\_file).ga Galaxy-Workflow-3)_COVID-19\_\_variation\_analysis\_reporting_(imported\_from\_uploaded\_file).ga ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [February 7, 2022, 7:53am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/10 "2022-02-07T07:53:35Z")
Hi Kathleen, > [@Kathleen\_Subramoney](#): > > The ivar trim step gives the following info: > Found 198 primers in BED file > No affected primer binding sites found! Found 198 primers in BED file Writing to removed\_reads.bam Number of references: 1 Reference Name: NC\_045512.2 Reference Length: 29903 Using Region: NC\_045512.2 Sorted By Coordinate This doesn’t seem to be the output of ivar _trim_ but of ivar _removereads_. What we would need is all the details of the ivar trim step, in particular, the input files and standard error and output. ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [March 18, 2022, 5:59am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/11 "2022-03-18T05:59:42Z")
Good day, I am attempting to run fast files generated from MiNION platform. I wanted to find out if the “COVID-19: variation analysis of ARTIC ONT” is the correct workflow to use? My aim is to generate an output that will provide the frequencies of each of the amino acids variations across the reads similar to the variant frequency generated from the Illumina workflow. Kind Regards Kathleen ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [March 18, 2022, 8:46am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/12 "2022-03-18T08:46:57Z")
Yes, that’s the right workflow. Make sure you’re using version 0.3 of it (or 0.3.1, which is functionally equivalent). This workflow is compatible with the IWC variant reporting and consensus workflows (just like the Illumina one). Keep in mind, that though well tested and running stably, the ONT WF probably has a lot more room for improvement on the analytical side. So feel encouraged to propose enhancements. Best, Wolfgang ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [March 18, 2022, 9:07am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/13 "2022-03-18T09:07:22Z")
Perfect. Thanks Wolfgang. Kind Regards Kathleen ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [April 5, 2022, 3:57pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/14 "2022-04-05T15:57:41Z")
Good day, I am trying to upload my fast files via FTP. I downloaded FileZilla and entered the [ftp.usegalaxy.eu](http://ftp.usegalaxy.eu) and my login details and completed uploads as seen below. I went to [galaxy.eu](http://galaxy.eu) and selected “choose remote files” and selected the ftp directory for the first 3 fastq files as a test. The upload seemed to have failed (second screenshot below). The error is "Failed to fetch url gxftp://Illumina fastq/K018630\_S2\_L001\_R2\_001.fastq.gz. [Errno 2] No such file or directory: '/[data/jwd/incoming/kathleen.subramoney@nhls.ac.za](mailto:data/jwd/incoming/kathleen.subramoney@nhls.ac.za)/Illumina fastq/K018630\_S2\_L001\_R2\_001.fastq.gz’ I selected fastqsanger.gz faster choosing the ftp files but it still does not recognise the files. Kindly assist if possible. Kind Regards Kathleen ![]() ![]() (Attachment PastedGraphic-2.tiff is missing) (Attachment PastedGraphic-1.tiff is missing) ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 5, 2022, 7:19pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/15 "2022-04-05T19:19:47Z")
Your screenshots are missing @Kathleen_Subramoney ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 5, 2022, 7:26pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/16 "2022-04-05T19:26:35Z")
The server is aware of your files it seems. What happens if, in the upload manager, you go into the “Illumina fastq” folder, select all in there, then upload? Do you again get that error? Or was this temporary? ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [April 6, 2022, 6:34am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/17 "2022-04-06T06:34:28Z")
Sorry about the screenshots. Galaxy emails seems to remove them after I send the email. I managed to resolve the issue. I tried this morning with more recent fastq files and seems to upload from FTP into galaxy perfectly. I think it was the format of the fastq that was incorrect. The extension was .fastq.gz but when I changed it to just .gz it worked. ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [April 12, 2022, 1:28pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/18 "2022-04-12T13:28:15Z")
Dear Wolfgang, I used the “COVID-19: variation analysis of ARTIC ONT” workflow earlier in March just after our previous communication, and it worked well with no errors. I have been trying to run a few fastq files this past 2 weeks and keep getting the same error under adjusted variant calls within primer binding sites: "parameter ‘genome\_file\_opts\_selector’: an invalid option (None) was selected, please verify”. I thought maybe it was my fastq input so a tried running a files that I ran previously that was successful but the same error occurs and the jobs afterwards are paused automatically and won’t continue even if I resume paused jobs. I tried both 0.3 and 0.3.1 but the same error occurs. Is there an issue with the workflow? Kind Regards Kathleen ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 13, 2022, 1:51pm UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/19 "2022-04-13T13:51:10Z")
Hmm, could it be that you don’t have the right version of bedtools installed and the WF is silently falling back to an older version? ---
**Author:** ![Kathleen\_Subramoney](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kathleen_subramoney/32/3053_2.png) [@Kathleen\_Subramoney](https://help.galaxyproject.org/u/Kathleen_Subramoney)\ **Post date:** [April 14, 2022, 5:29am UTC](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342/20 "2022-04-14T05:29:53Z")
I use the same bed tools for the Illumina workflow and it works. I will double check if the ones I am using are the latest versions and try running the workflow again. [Next page](https://help.galaxyproject.org/t/sars-cov-2-arctic-v4-files/7342.md?page=2)