parsing error in WGS single sample workflow

[mmwheel]

After digging further into this [issue]( ( #1331 (comment)). Short reads (<75bp) cause the smith waterman algorithm in the DRAGMAP aligner to crash. When I filter out these short reads and their mates the parsing error goes away and alignment proceeds. It looks like Illumina is aware of the issue and implemented a fix a while ago in DRAGMAP v1.3.0 (see: https://github.com/Illumina/DRAGMAP/releases). Is it possible for WARP to update the DRAGMAP version in their WGS single sample pipeline?

Thanks,

[ekiernan]

@mmwheel the team is actively working on this update.

[nikellepetrillo]

Hi @mmwheel ,

Thanks for sharing your findings on the short read issue with DRAGMAP. I attempted to update our DRAGMAP version to 1.3.0, but now we're encountering a similar error:

[E::sam_parse1] invalid QUAL character
[W::sam_read1] Parse error at line 3380
samtools view: error reading file "-"

I’ve increased the memory and disk allocation, but the issue persists.

Additionally, we noticed that the most recent commit in the DRAGMAP repo is titled "patch 1.3.1- gba85597c mapq0 fix", which might be relevant: Illumina/DRAGMAP@c4cb6c9#diff-d9c6b7ad082ecc892922063a8ce5123b24e71bac93f2ef9a866675231b76787a

I also noticed that DRAGMAP 1.3.1 has not been officially released yet, so there’s no confirmed fix available beyond 1.3.0.

Given that, we are unable to investigate this further at this time. However, if you come across any updates or workarounds, we would love to hear about them!

-Nikelle

[mmwheel]

Hi Nikelle, Thank you for looking into this. Did you by chance make a docker image of DRAGMAP 1.3.1? Also wondering if you think DRAGMAP 1.3.1 is substantially different from the version currently implemented by WARP -- enough to cause batch effects in the data? Thanks again, Marsha

…

On Fri, Apr 4, 2025 at 7:53 AM Nikelle Petrillo ***@***.***> wrote: Hi @mmwheel <https://github.com/mmwheel> , Thanks for sharing your findings on the short read issue with DRAGMAP. I attempted to update our DRAGMAP version to 1.3.0, but now we're encountering a similar error: [E::sam_parse1] invalid QUAL character [W::sam_read1] Parse error at line 3380 samtools view: error reading file "-" I’ve increased the memory and disk allocation, but the issue persists. Additionally, we noticed that the most recent commit in the DRAGMAP repo is titled "patch 1.3.1- gba85597c mapq0 fix", which might be relevant: ***@***.*** #diff-d9c6b7ad082ecc892922063a8ce5123b24e71bac93f2ef9a866675231b76787a <Illumina/DRAGMAP@c4cb6c9#diff-d9c6b7ad082ecc892922063a8ce5123b24e71bac93f2ef9a866675231b76787a> I also noticed that DRAGMAP 1.3.1 has not been officially released yet, so there’s no confirmed fix available beyond 1.3.0. Given that, we are unable to investigate this further at this time. However, if you come across any updates or workarounds, we would love to hear about them! -Nikelle — Reply to this email directly, view it on GitHub <#1538 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKYXRPZI7DES62T7QPNURXD2X2MHJAVCNFSM6AAAAABYPMEA62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZYHE3DMMZSHE> . You are receiving this because you were mentioned.Message ID: ***@***.***> [image: nikellepetrillo]*nikellepetrillo* left a comment (broadinstitute/warp#1538) <#1538 (comment)> Hi @mmwheel <https://github.com/mmwheel> , Thanks for sharing your findings on the short read issue with DRAGMAP. I attempted to update our DRAGMAP version to 1.3.0, but now we're encountering a similar error: [E::sam_parse1] invalid QUAL character [W::sam_read1] Parse error at line 3380 samtools view: error reading file "-" I’ve increased the memory and disk allocation, but the issue persists. Additionally, we noticed that the most recent commit in the DRAGMAP repo is titled "patch 1.3.1- gba85597c mapq0 fix", which might be relevant: ***@***.*** #diff-d9c6b7ad082ecc892922063a8ce5123b24e71bac93f2ef9a866675231b76787a <Illumina/DRAGMAP@c4cb6c9#diff-d9c6b7ad082ecc892922063a8ce5123b24e71bac93f2ef9a866675231b76787a> I also noticed that DRAGMAP 1.3.1 has not been officially released yet, so there’s no confirmed fix available beyond 1.3.0. Given that, we are unable to investigate this further at this time. However, if you come across any updates or workarounds, we would love to hear about them! -Nikelle — Reply to this email directly, view it on GitHub <#1538 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKYXRPZI7DES62T7QPNURXD2X2MHJAVCNFSM6AAAAABYPMEA62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZYHE3DMMZSHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[nikellepetrillo]

Hi Marsha,

We didn’t create a Docker image for DRAGMAP 1.3.1 and haven’t evaluated it in our pipelines. Unfortunately, we’re not able to create the Docker or run an evaluation ourselves at this time.

That said, if you’re interested in trying it out, we’d definitely welcome the contribution. If you end up creating a Docker image and testing it, feel free to fork the WARP repo, make the necessary changes, and open a pull request—we’d be more than happy to take a look.

Thank you!
Nikelle