Unable to import tsv file in DNAnexus platform

Hail Query & hailctl
#1

Hi,

I am unable to read a phenotype file(tsv format, tab delimited) from project file system. I am getting the below error:

FatalError: IOException: Server returned HTTP response code: 416 for URL: http://10.0.3.1:8090/DB/R/database-G90zjk8JpPj11j2Y5q5Yq2v2/bmrn-hpc-scratch-bucket/norm_ht_phens_SAIGE.tsv

Java stack trace:
java.io.IOException: Server returned HTTP response code: 416 for URL: http://10.0.3.1:8090/DB/R/database-G90zjk8JpPj11j2Y5q5Yq2v2/bmrn-hpc-scratch-bucket/norm_ht_phens_SAIGE.tsv

I tried reading it from the cluster itself, however I got the file not found error:

FatalError: FileNotFoundException: File file:/opt/notebooks/norm_ht_phens_SAIGE.tsv does not exist

Any thoughts?

#2

You can do hadoop fs -put /opt/notebooks/norm_ht_phens_SAIGE.tsv /tmp followed by hl.import_table("tmp/norm_ht_phens_SAIGE.tsv") or something along those lines. There is likely a better way.