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ComparativeGenomicsToolkit / Comparative-Annotation-Toolkit

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Error at filter_transmap.py #305

Open cbcunningham opened 9 months ago

cbcunningham commented 9 months ago

Hi,

I seem to be hitting the an error. This does not appear using the test data and my gff3s return no errors or warnings when using validate_gff3.

[2023-12-06T12:40:12-0500] [MainThread] [I] [cat] Filtering transMap PSL for Nv_n. ERROR: [pid 3089496] Worker Worker(salt=7024222896, workers=1, host=ra2-22, username=cbc83, pid=3089496) failed Task: FilterTransMap for Nv_n Traceback (most recent call last): File "/apps/eb/Comparative-Annotation-Toolkit/2.2.1-foss-2020b/lib/python3.8/site-packages/luigi/worker.py", line 203, in run new_deps = self._run_get_new_deps() File "/apps/eb/Comparative-Annotation-Toolkit/2.2.1-foss-2020b/lib/python3.8/site-packages/luigi/worker.py", line 138, in _run_get_new_deps task_gen = self.task.run() File "/apps/eb/Comparative-Annotation-Toolkit/2.2.1-foss-2020b/lib/python3.8/site-packages/cat/init.py", line 1412, in run resolved_df = filter_transmap(tm_args.tm_psl, tm_args.ref_psl, tm_args.tm_gp, File "/apps/eb/Comparative-Annotation-Toolkit/2.2.1-foss-2020b/lib/python3.8/site-packages/cat/filter_transmap.py", line 164, in filter_transmap coding_merged_df, coding_collapse_filtered = filter_clusters(coding_clustered, transcript_gene_map, File "/apps/eb/Comparative-Annotation-Toolkit/2.2.1-foss-2020b/lib/python3.8/site-packages/cat/filter_transmap.py", line 340, in filter_clusters if best_clusters[0] in cluster_done: NameError: name 'cluster_done' is not defined

Any guidance would be appreciated. I can provide any input or output files for reference.

Thanks, Chris

cbcunningham commented 3 months ago

Dylan,

No, I never did figure it out. I just moved on to a different program.

Best, Chris

On Wed, May 22, 2024 at 12:09 PM Dylan DeBaun @.***> wrote:

Hi @cbcunningham https://github.com/cbcunningham , Did you figure this out? I just got the same error. Best, Dylan

— Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/305#issuecomment-2125173996, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7XQED2OGM2TIMNPV22R5TZDS7MFAVCNFSM6AAAAABAJZGC2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRVGE3TGOJZGY . You are receiving this because you were mentioned.Message ID: <ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/305/2125173996 @github.com>

dylandebaun commented 3 months ago

Hi Chris, Thanks, the filter_transmap.py was updated recently and that fixed the issue for me! Best, Dylan