<div dir="ltr">Perhaps makeblastdb itself failed (and our wrapper didn't notice)? Those are the first files looked for after calling makeblastdb, to see if it could make a BLAST database. Are there any GenBank/NC_005816.fna.n* or GenBank/NC_005816.faa.p* files present?<div><br></div><div>If it helps, the commands our script was trying to run were:</div><div><br></div><div>$ makeblastdb -dbtype nucl -in GenBank/NC_005816.fna \</div><div>-parse_seqids -hash_index -max_file_sz 20MB -taxid 10<br></div><div><br></div><div>and:</div><div><br></div><div>$ makeblastdb -dbtype prot -in GenBank/NC_005816.faa \</div><div>-parse_seqids -hash_index -max_file_sz 20MB -taxid 10<br></div><div><br></div><div>I'm not sure I have remote access to any 32bit machines right now...</div><div><br></div><div>Peter</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, May 16, 2020 at 2:22 PM Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Control: tags -1 upstream<br>
Control: forwarded -1 Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
<br>
Hi Peter,<br>
<br>
it seems the patch applied does not work for 32bit architectures.<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
On Sat, May 16, 2020 at 02:25:20PM +0300, Adrian Bunk wrote:<br>
> Source: python-biopython<br>
> Version: 1.76+dfsg-2<br>
> Severity: serious<br>
> Tags: ftbfs<br>
> <br>
> <a href="https://buildd.debian.org/status/package.php?p=python-biopython&suite=sid" rel="noreferrer" target="_blank">https://buildd.debian.org/status/package.php?p=python-biopython&suite=sid</a><br>
> <br>
> ...<br>
> ======================================================================<br>
> FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB)<br>
> Test makeblastdb wrapper with nucleotide database.<br>
> ----------------------------------------------------------------------<br>
> Traceback (most recent call last):<br>
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 249, in test_fasta_db_nucl<br>
> self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhd"))<br>
> AssertionError: False is not true<br>
> <br>
> ======================================================================<br>
> FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB)<br>
> Test makeblastdb wrapper with protein database.<br>
> ----------------------------------------------------------------------<br>
> Traceback (most recent call last):<br>
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 208, in test_fasta_db_prot<br>
> self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))<br>
> AssertionError: False is not true<br>
> <br>
> ----------------------------------------------------------------------<br>
> Ran 518 tests in 330.272 seconds<br>
> <br>
> FAILED (failures = 1)<br>
> Skipping any tests requiring internet access<br>
> Python version: 3.8.3 (default, May 14 2020, 11:03:12) <br>
> [GCC 9.3.0]<br>
> Operating system: posix linux<br>
> E: pybuild pybuild:352: test: plugin custom failed with: exit code=1: set -e; \<br>
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home; \<br>
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc/examples; \<br>
> cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \<br>
> cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \<br>
> cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \<br>
> cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; \<br>
> cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests; \<br>
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py --offline<br>
> dh_auto_test: error: pybuild --test -i python{version} -p 3.8 --test --system=custom "--test-args=set -e; \\\<br>
> mkdir -p {build_dir}/home; \\\<br>
> mkdir -p {build_dir}/Doc/examples; \\\<br>
> cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\<br>
> cp -a Doc/Tutorial {build_dir}/Doc; \\\<br>
> cp -a Doc/examples {build_dir}/Doc; \\\<br>
> cp -a Tests {build_dir}; \\\<br>
> cd {build_dir}/Tests; \\\<br>
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" returned exit code 13<br>
> make[1]: *** [debian/rules:83: override_dh_auto_test] Error 25<br>
> <br>
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</blockquote></div>