IgBLAST crashes in docker container

[antonkulaga]

When I ran the latest docker container on test fastq data it crashes with IgBLAST subprocess
stdout.txt
stderr.txt

Here is the command that was run:

bracer assemble --ncores 28 --species Hsap  cell_1 bracer_results /cromwell-executions/BCR_extraction/39483cc3-3a87-4370-96bb-7c7e8e4112dd/call-bracer_assemble/inputs/1726693592/cell1_1.fastq /cromwell-executions/BCR_extraction/39483cc3-3a87-4370-96bb-7c7e8e4112dd/call-bracer_assemble/inputs/1726693592/cell1_2.fastq

[dcroote]

This may have to do with the IGDATA environment variable being exported by a Dockerfile ENTRYPOINT script:

bracer/Dockerfile

Line 72 in 131c2b9

ENTRYPOINT ["bash", "/bracer/docker_helper_files/docker_wrapper.sh"]

Try exporting IGDATA prior to running bracer assemble:

export IGDATA=/ncbi-igblast-1.4.0/bin && bracer assemble ...