hillerlab make_lastz_chains issues

hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz

MIT License

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issues

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Using an alternative scoring matrix in make_lastz_chains v.2.0.8

#68 ohdongha opened 3 weeks ago
2
A minor discrepancy between v1.0.0 and v2.0.8 at 'fill_chain' step

#67 ohdongha opened 3 weeks ago
4
chainCleaner failure with chromosomes >1Gb (2^30)

#66 ohdongha closed 3 weeks ago
11
lastz step terminated with an error exit status (132)

#65 munegowda opened 3 months ago
1
The number of tasks submitted by SLURM exceeded the limit

#64 aaannaw opened 3 months ago
16
Error: detected space-or-tab-containing sequence

#63 ecbaker7-tamu closed 4 months ago
3
TypeError: 'bool' object is not iterable

#62 bioluria opened 4 months ago
2
Some problems during execution

#61 duan12345678 opened 5 months ago
1
PBSpro support

#60 mictadlo opened 5 months ago
7
Speed up task processing

#59 molinfzl opened 5 months ago
3
speeding up/parallelizing make_chains.py with Slurm: NOTE: Error submitting process 'execute_jobs (##)' for execution -- Execution is retried

#58 SomePersonSomeWhereInTheWorld opened 6 months ago
3
pipeline fails clean chain step - ERROR: cannot create a tempfile for netting the chain file: Permission denied

#57 d6948739 opened 6 months ago
1
Alignment of a large genome in 2bit

#56 ohdongha opened 7 months ago
1
chain_run error

#55 LliliansCalvo opened 7 months ago
2
setup_genome_sequences fails if rerunning from the "cat" step

#54 ning-y opened 8 months ago
1
Allow custom JOB_TIME_REQ

#53 ning-y closed 1 month ago
3
Allow custom process.time

#52 ning-y closed 1 month ago
0
V2 pipeline errors (cat_step; with my data NOT with test_data); V1 pipeline error:pipeline crashed

#51 vinitamehlawat opened 8 months ago
5
The pipeline crashed Error

#50 vinitamehlawat opened 8 months ago
0
unable to run make lastz chains on slurm cluster- where do I edit config file?

#49 pfb2201 closed 8 months ago
1
NOTE: Process `execute_jobs (605)` terminated with an error exit status (1) -- Execution is retried (1)

#48 kuangzhuoran opened 9 months ago
2
Is there any parameter to set the maximum number of threads used?

#47 kuangzhuoran opened 9 months ago
0
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 vinitamehlawat opened 10 months ago
0
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

#45 SomePersonSomeWhereInTheWorld opened 10 months ago
2
Pipeline failed at last clean_chains step

#44 Alchimic007 opened 11 months ago
7
Partial Lastz Process Timeouts in make_lastz_chains

#43 ZhaoHang-bio opened 11 months ago
0
Fragmented genomes

#42 giovannaVeiga opened 12 months ago
3
Fatal non-specific error if genome names are the same as genome filenames

#41 ning-y opened 12 months ago
1
Fix missing double-quotes giving argparse error

#40 ning-y closed 12 months ago
1
Multiple Alignments

#39 lutfia95 opened 1 year ago
1
TODO: add param to customise queue parameter

#38 kirilenkobm closed 1 year ago
1
Fixing issue #35 + some additional changes - see changelog

#37 kirilenkobm closed 1 year ago
0
issue in the lastz step

#36 lnyawen closed 1 year ago
8
Argument list too long - lastz

#35 AgustoLuz closed 9 months ago
8
Issue Running make_lastz_chains-2.0.6 on Test Data

#34 ZhaoHang-bio closed 1 year ago
7
TODO? QC/statistics module

#33 kirilenkobm opened 1 year ago
0
The pipeline does not work with 2bit files as input

#32 kirilenkobm closed 1 year ago
1
self chains

#31 BoBo2021jenny opened 1 year ago
2
All temp files are regulated

#30 kirilenkobm closed 1 year ago
0
Fixed partitioning

#29 kirilenkobm closed 1 year ago
0
Full scale run creates too many lastz jobs

#28 kirilenkobm closed 1 year ago
1
Rearrangement

#27 kirilenkobm closed 1 year ago
0
Uncaught exception from user code: Command failed.

#26 igorpop0v closed 1 year ago
10
Error running make_lastz_chains on Slurm cluster

#25 philge closed 1 year ago
6
requirements

#24 ebioman closed 1 year ago
1
nextflow

#23 BoBo2021jenny closed 1 year ago
1
RepeatFiller

#22 Sandhyash closed 1 year ago
1
Error in 'lastz'

#21 hongbingp closed 1 year ago
12
The issue with the temporary file generation path.

#20 hcsun1 closed 1 year ago
1
alignment is taking too long

#19 gunjanpandey closed 1 year ago
4