Samtools error:[E::bam_hdr_write] Header too long for BAM format

[linkmonica]

Hi

When I run bamsrugeon-20200925-python-3.8.1, I get this error [E::bam_hdr_write] Header too long for BAM format, which I suspect coming from samtools/1.10. So I tried using samtools/1.9 instead and I don't get any errors, but I don't even see spike-in mutations in the data. When I use a small number of spike-in mutations they do run without any errors and with spike-in.
As I want to insert a huge number of mutations, bamsurgeon fails with the above error. Any suggestions that may help with this issue?

Thanks.
Monica

[adamewing]

Hi Monica,

Are the mutations you're trying to make close together e.g. within 1000bp of each other?

If so, try setting the -z option to something around your read length (~100-150bp probably).

It would also help troubleshoot if you post the output from addsnv.

Good luck!

[linkmonica]

Hi Adam, I tried using -z option as well, but I still see the error. I can try post the details of addsnv. [E::bam_hdr_write] Header too long for BAM format samtools merge: failed to write header to "addsnv.b0ed8228-36ee-43d0-8cde-8e1a5a48fc15.muts.bam": No such file or directory INFO 2021-06-09 12:35:59,164 done making mutations, merging mutations into BM.bam --> BM.withamperrors.bam Traceback (most recent call last): File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/bamsurgeon/20200925-python-3.8.1/bin/addsnv.py", line 4, in <module>

…

__import__('pkg_resources').run_script('bamsurgeon==1.2', 'addsnv.py') File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/45.1.0-python-3.8.1/lib/python3.8/site-packages/setuptools-45.1.0-py3.8.egg/pkg_resources/__init__.py", line 667, in run_script File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/45.1.0-python-3.8.1/lib/python3.8/site-packages/setuptools-45.1.0-py3.8.egg/pkg_resources/__init__.py", line 1470, in run_script File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/bamsurgeon/20200925-python-3.8.1/lib/python3.8/site-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsnv.py", line 523, in <module> File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/bamsurgeon/20200925-python-3.8.1/lib/python3.8/site-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsnv.py", line 520, in run File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/bamsurgeon/20200925-python-3.8.1/lib/python3.8/site-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsnv.py", line 466, in main File "/opt/cesga/easybuild-cesga/software/Compiler/gcccore/6.4.0/bamsurgeon/20200925-python-3.8.1/lib/python3.8/site-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsnv.py", line 78, in replace File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__ File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file does not contain alignment data as the header is too long it does not generate bam file I think.

On Mon, Jun 7, 2021 at 7:16 AM adamewing ***@***.***> wrote: Hi Monica, Are the mutations you're trying to make close together e.g. within 1000bp of each other? If so, try setting the -z option to something around your read length (~100-150bp probably). It would also help troubleshoot if you post the output from addsnv. Good luck! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#181 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIOM2DJ5V4VOX7ECLTEJVFDTRRIZFANCNFSM456HGGIA> .

-- Monica Valecha, PhD Student Phylogenomics Lab, University of Vigo http://darwin.uvigo.es/