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Issues: hillerlab/make_lastz_chains

Stalled at the doChainRun step
#10 opened Oct 17, 2022 by ohdongha
Open 6
issue in the lastz step
#36 by lnyawen was closed Oct 27, 2023
Closed 8
Multiple Alignments
#39 opened Oct 26, 2023 by lutfia95
Open 1
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23 Open 32 Closed
23 Open 32 Closed
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Issues list

Some problems during execution
#61 opened May 10, 2024 by duan12345678
1
PBSpro support
#60 opened May 9, 2024 by mictadlo
7
Speed up task processing
#59 opened May 8, 2024 by molinfzl
speeding up/parallelizing make_chains.py with Slurm: NOTE: Error submitting process 'execute_jobs (##)' for execution -- Execution is retried
#58 opened Apr 30, 2024 by SomePersonSomeWhereInTheWorld
3
pipeline fails clean chain step - ERROR: cannot create a tempfile for netting the chain file: Permission denied
#57 opened Apr 19, 2024 by d6948739
1
Alignment of a large genome in 2bit
#56 opened Mar 19, 2024 by ohdongha
1
chain_run error
#55 opened Mar 15, 2024 by LliliansCalvo
2
setup_genome_sequences fails if rerunning from the "cat" step
#54 opened Feb 28, 2024 by ning-y
1
Allow custom process.time
#52 opened Feb 18, 2024 by ning-y
1
V2 pipeline errors (cat_step; with my data NOT with test_data); V1 pipeline error:pipeline crashed
#51 opened Feb 14, 2024 by vinitamehlawat
5
The pipeline crashed Error
#50 opened Feb 14, 2024 by vinitamehlawat
NOTE: Process execute_jobs (605) terminated with an error exit status (1) -- Execution is retried (1) bug Something isn't working nextflow issues Nextflow issues
#48 opened Jan 27, 2024 by kuangzhuoran
2
Is there any parameter to set the maximum number of threads used?
#47 opened Jan 18, 2024 by kuangzhuoran
An error occurred while executing cat: Error! No non-empty files found at /home/vlamba/CotDis_chaining/temp_concat_lastz_output. The failed operation label is: cat_step
#46 opened Dec 29, 2023 by vinitamehlawat
make_chains.py in pipeline: modules.error_classes.PipelineFileNotFoundError: Error! No non-empty files found at make_lastz_chains/test_out/temp_concat_lastz_output. The failed operation label is: cat_step bug Something isn't working
#45 opened Dec 14, 2023 by SomePersonSomeWhereInTheWorld
2
Pipeline failed at last clean_chains step
#44 opened Nov 30, 2023 by Alchimic007
5
Partial Lastz Process Timeouts in make_lastz_chains
#43 opened Nov 29, 2023 by ZhaoHang-bio
Fragmented genomes
#42 opened Nov 8, 2023 by giovannaVeiga
3
Fatal non-specific error if genome names are the same as genome filenames bug Something isn't working
#41 opened Nov 6, 2023 by ning-y
1
Multiple Alignments documentation Improvements or additions to documentation
#39 opened Oct 26, 2023 by lutfia95
1
TODO? QC/statistics module enhancement New feature or request
#33 opened Sep 21, 2023 by kirilenkobm
self chains enhancement New feature or request
#31 opened Sep 17, 2023 by BoBo2021jenny
2
Stalled at the doChainRun step documentation Improvements or additions to documentation performance Everything related to the pipeline performance
#10 opened Oct 17, 2022 by ohdongha
6
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