Error with cramtools 3.0 - Error downloading ref and exception handle

[Prathyusha-konda]

Hello,

I have been coming across errors with cramtools, similar to what is mentioned here (#55).

I tried the following (#55)

Use JAVA 8
to download latest cramtools jar: wget 'https://github.com/enasequence/cramtools/blob/master/cramtools-3.0.jar?raw=true' -O cramtools-3.0.jar
to check version: java -jar cramtools-3.0.jar | grep Version
to check if the class is in the jar file: jar tf cramtools-3.0.jar | grep CountingOutputStream

However, this didn't help. I also noticed errors while downloading the reference sequences.

Adding ref pattern: http://www.ebi.ac.uk/ena/cram/md5/%s
ERROR 2017-10-10 17:45:19 ReferenceSource Downloaded sequence is corrupt: requested md5=bb9dae7b38a25a45dae8e3179d7c4241, received md5=d41d8cd98f00b204e9800998ecf8427e
.
.
followed by the exception handle.

Could you please help me figure this out?

Thank you,
Prathyusha

[tk2]

Hi Prathyusha - I think (haven't confirmed yet) that the error has come from the CRAM reference registry now using https, and cramtools has not been patched yet for this. In the meantime, you can use Samtools to do the conversion - but Samtools must be built with lib-curl enabled (to overcome the new requirement for https).