From 4d0d29a37b9056d843ec6c775afa009fe3d45fd3 Mon Sep 17 00:00:00 2001
From: Luiz Irber <luiz.irber@gmail.com>
Date: Sat, 30 May 2020 14:09:42 -0700
Subject: [PATCH] disable multithreading in fastq-dump

---
 Dockerfile                       | 2 +-
 wort/blueprints/compute/tasks.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 586fbdd..c11fd91 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.7.1-slim-stretch
+FROM python:3.8.3-slim-buster
 
 RUN groupadd user && \
     useradd --create-home --home-dir /home/user -g user -s /bin/bash user
diff --git a/wort/blueprints/compute/tasks.py b/wort/blueprints/compute/tasks.py
index 4bc1140..60f6360 100644
--- a/wort/blueprints/compute/tasks.py
+++ b/wort/blueprints/compute/tasks.py
@@ -38,7 +38,7 @@ def compute(sra_id):
     with NamedTemporaryFile("w+b") as f:
         try:
             shell(
-                "fastq-dump --fasta 0 --skip-technical --readids --read-filter pass --dumpbase --clip --split-e -Z {sra_id} | "
+                "fastq-dump --disable-multithreading --fasta 0 --skip-technical --readids --read-filter pass --dumpbase --clip --split-e -Z {sra_id} | "
                 "sourmash compute -k 21,31,51 "
                 "  --scaled 1000 "
                 "  --track-abundance "