pysam.fastq: OSError: [Errno 9] Bad file descriptor

[schorlton]

Getting OSError: [Errno 9] Bad file descriptor when trying to use pysam as a samtools wrapper. Full reproduction:

docker run -it --rm \
    -u root \
    -v $(pwd):/work \
    -w /work \
    mambaorg/micromamba@sha256:1d05a8a7d88142f8225927756272748bc5feb438c0185de362e98ae5d88bf2f4 \
    bash

micromamba install pysam==0.21.0 -c bioconda -c conda-forge -c defaults

cat test.sam 
HWI-EAS240_0001:2:1:1144:15181#0	4	*	0	0	*	*	0	0	CTCAGGTGGCTTCCAACATTGGGATGAGTAACGTTAGNCATGTGTCAAGATCGGAAGANNGGTTCAGCAGGAATGC	bbbabbbbbbbbabbbabbabbbabbbbb`bbbb`VWBVUWWVZXZbYbXb_bbbOOGBBOOOOO\\VX`bbbbbb

>>> import pysam
>>> pysam.fastq("-0", "test.fastq", "test.sam")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
OSError: [Errno 9] Bad file descriptor
>>> 
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
OSError: [Errno 9] Bad file descriptor

However, samtools works:

micromamba install -y samtools==1.17 -c conda-forge -c bioconda -c defaults

samtools fastq -0 samtools.fastq test.sam 
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 1 reads
(base) root@f11037699062:/work# cat samtools.fastq 
@HWI-EAS240_0001:2:1:1144:15181#0
CTCAGGTGGCTTCCAACATTGGGATGAGTAACGTTAGNCATGTGTCAAGATCGGAAGANNGGTTCAGCAGGAATGC
+
bbbabbbbbbbbabbbabbabbbabbbbb`bbbb`VWBVUWWVZXZbYbXb_bbbOOGBBOOOOO\\VX`bbbbbb

Thanks for your help!