New issue with Indels

[gafishbein]

Thank you so much for creating sigProfiler. In the last month I reinstalled sigProfiler (I don't recall when I initially installed it, sorry) and I suddenly get errors when extracting indels (SBS and DBS are unaffected). I have reproduced this on 3 computers. VCF files I successfully used in the past now give this traceback message:

Traceback (most recent call last): File "", line 1, in File "SigProfilerExtractor\sigpro.py", line 862, in sigProfilerExtractor decomp.spa_analyze(allgenomes, output, signatures=processAvg, genome_build=genome_build, cosmic_version=cosmic_version, exome=exome, verbose=False, File "SigProfilerAssignment\decomposition.py", line 306, in spa_analyze genomes = sigPlot.process_input(genomes, m) File "sigProfilerPlotting\sigProfilerPlotting.py", line 213, in process_input return order_input_context(plot_type, data) File "sigProfilerPlotting\sigProfilerPlotting.py", line 207, in order_input_context reindexed_data = input_data.reindex(ref_format) File "pandas\util_decorators.py", line 324, in wrapper return func(*args, **kwargs) File "pandas\core\frame.py", line 4807, in reindex return super().reindex(**kwargs) File "pandas\core\generic.py", line 4966, in reindex return self._reindex_axes( File "pandas\core\frame.py", line 4626, in _reindex_axes frame = frame._reindex_index( File "pandas\core\frame.py", line 4645, in _reindex_index return self._reindex_with_indexers( File "pandas\core\generic.py", line 5032, in _reindex_with_indexers new_data = new_data.reindex_indexer( File "pandas\core\internals\managers.py", line 676, in reindex_indexer self.axes[axis]._validate_can_reindex(indexer) File "pandas\core\indexes\base.py", line 4121, in _validate_can_reindex raise ValueError("cannot reindex on an axis with duplicate labels") ValueError: cannot reindex on an axis with duplicate labels

Thanks!

[mdbarnesUCSD]

Hi @gafishbein,

Could you please let us know what versions of SigProfiler packages you have installed in your environment? Also, can you please confirm that running from a new directory with just your vcf files that the error does not persist?

Thanks!

[gafishbein]

Thank you so much for getting back to me. I can confirm that running from a new directory with just my vcf files creates the same error. I am using the following (unfortunately, I don't recall which versions I was using when it was functioning).

sigProfilerExtractor: 1.1.23 sigProfilerMatrixGenerator: 1.2.25 sigProfilerPlotting: 1.3.21 sigProfilerAssignment: 0.1.3

Thanks again for your assistance!

On Fri, Mar 8, 2024 at 9:02 AM mdbarnesUCSD @.***> wrote:

Hi @gafishbein https://github.com/gafishbein,

Could you please let us know what versions of SigProfiler packages that you have installed in your environment? Also, can you please confirm that running from a new directory with just your vcf files that the error does not persist?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/AlexandrovLab/SigProfilerExtractor/issues/236#issuecomment-1986070123, or unsubscribe https://github.com/notifications/unsubscribe-auth/BGYZBGZTHAMDHA25RKJAGOTYXHVLRAVCNFSM6AAAAABELUOFWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGA3TAMJSGM . You are receiving this because you were mentioned.Message ID: @.***>

[gafishbein]

Thanks again for your assistance. I was able to find output from a previous successful attempt at ID analysis. Here were the versions that worked. Running the newer versions on the same data fail.

Python Version: 3.9.12 SigProfilerExtractor Version: 1.1.21 SigProfilerPlotting Version: 1.3.10 SigProfilerMatrixGenerator Version: 1.2.13 SigProfilerAssignment Version: 0.0.25

Greg

On Fri, Mar 8, 2024 at 1:13 PM Gregory A. Fishbein < @.***> wrote:

Thank you so much for getting back to me. I can confirm that running from a new directory with just my vcf files creates the same error. I am using the following (unfortunately, I don't recall which versions I was using when it was functioning).

sigProfilerExtractor: 1.1.23 sigProfilerMatrixGenerator: 1.2.25 sigProfilerPlotting: 1.3.21 sigProfilerAssignment: 0.1.3

Thanks again for your assistance!

On Fri, Mar 8, 2024 at 9:02 AM mdbarnesUCSD @.***> wrote:

Hi @gafishbein https://github.com/gafishbein,

Could you please let us know what versions of SigProfiler packages that you have installed in your environment? Also, can you please confirm that running from a new directory with just your vcf files that the error does not persist?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/AlexandrovLab/SigProfilerExtractor/issues/236#issuecomment-1986070123, or unsubscribe https://github.com/notifications/unsubscribe-auth/BGYZBGZTHAMDHA25RKJAGOTYXHVLRAVCNFSM6AAAAABELUOFWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGA3TAMJSGM . You are receiving this because you were mentioned.Message ID: @.***>

[mdbarnesUCSD]

Thank you for providing this, we are looking into this issue and will update here.

[mdbarnesUCSD]

Hi @gafishbein,

I believe the issue was due to sigProfilerPlotting and was present in v.1.3.21. Could you please update to sigProfilerPlotting v1.3.22, which should now resolve this issue. Please reach out if you are still encountering it. Thank you!

[mdbarnesUCSD]

Please re-open this thread if you are still encountering this issue, thanks!

[gafishbein]

No more issues. Thanks for your assistance!!

On Fri, Apr 19, 2024 at 1:07 PM mdbarnesUCSD @.***> wrote:

Please re-open this thread if you are still encountering this issue, thanks!

— Reply to this email directly, view it on GitHub https://github.com/AlexandrovLab/SigProfilerExtractor/issues/236#issuecomment-2067215786, or unsubscribe https://github.com/notifications/unsubscribe-auth/BGYZBGZF2ZWP7HIQDU6Q6RLY6F2RBAVCNFSM6AAAAABELUOFWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRXGIYTKNZYGY . You are receiving this because you were mentioned.Message ID: @.***>