samstudio8 / dehumanizer Goto Github PK

Not an issue.

Hello,

I'm following the instructions and running the below command:

wget https://sam.s3.climb.ac.uk/dehumanizer/20210906/dehuman.20210906.map-ont.mmi

However, it's returning the below error:

Resolving sam.s3.climb.ac.uk (sam.s3.climb.ac.uk)... 137.205.52.6
Connecting to sam.s3.climb.ac.uk (sam.s3.climb.ac.uk)|137.205.52.6|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2021-12-02 12:16:30 ERROR 403: Forbidden.```

I've also tried with curl, which didn't work, and from multiple different servers. I think the problem is on your end?

Thanks,

Phil

Tried a dehumanizer 'polish' with reticulatus, but it broke downstream minimapping.

Turns out, on inspection, the output files looked like:

@contig_1:1.0-13849.0
AAAATGATGCCGCGCAGCTCCC...
+
None

I tried to download the pre-build manifests, but I ran into a couple of problems: first I get a warning that sam.s3.climb.ac.uk certificate has expired, then if I ignore the warning I get a 403 forbidden error. Is there somewhere else I can get them?

not sure why I'm submitting this as an issue because I literally have no more information other than I tried to run and got:

Segmentation fault

dehumanise /data/md1mpar/wc/dehumanizer/manifest.txt --bam SHEF-C243B.bam --preset map-ont -o SHEF-C243B-clean.bam --log SHEF-C243B-clean.bam.log

worked with a fastq, so maybe a problem with my bam?

because it breaks on gzip