disable multithreading in fastq-dump

sourmash-bio · May 30, 2020 · 4d0d29a · 4d0d29a
1 parent 1fb4a9f
commit 4d0d29a
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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 "