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hillerlab
/
make_lastz_chains
Portable solution to generate genome alignment chains using lastz
MIT License
41
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8
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lastz step terminated with an error exit status (132)
#65
munegowda
opened
20 hours ago
0
The number of tasks submitted by SLURM exceeded the limit
#64
aaannaw
opened
2 weeks ago
16
Error: detected space-or-tab-containing sequence
#63
ecbaker7-tamu
closed
1 month ago
3
TypeError: 'bool' object is not iterable
#62
bioluria
opened
1 month ago
0
Some problems during execution
#61
duan12345678
opened
2 months ago
1
PBSpro support
#60
mictadlo
opened
2 months ago
7
Speed up task processing
#59
molinfzl
opened
2 months ago
0
speeding up/parallelizing make_chains.py with Slurm: NOTE: Error submitting process 'execute_jobs (##)' for execution -- Execution is retried
#58
SomePersonSomeWhereInTheWorld
opened
3 months ago
3
pipeline fails clean chain step - ERROR: cannot create a tempfile for netting the chain file: Permission denied
#57
d6948739
opened
3 months ago
1
Alignment of a large genome in 2bit
#56
ohdongha
opened
4 months ago
1
chain_run error
#55
LliliansCalvo
opened
4 months ago
2
setup_genome_sequences fails if rerunning from the "cat" step
#54
ning-y
opened
5 months ago
1
Allow custom JOB_TIME_REQ
#53
ning-y
opened
5 months ago
3
Allow custom process.time
#52
ning-y
opened
5 months ago
0
V2 pipeline errors (cat_step; with my data NOT with test_data); V1 pipeline error:pipeline crashed
#51
vinitamehlawat
opened
5 months ago
5
The pipeline crashed Error
#50
vinitamehlawat
opened
5 months ago
0
unable to run make lastz chains on slurm cluster- where do I edit config file?
#49
pfb2201
closed
5 months ago
1
NOTE: Process `execute_jobs (605)` terminated with an error exit status (1) -- Execution is retried (1)
#48
kuangzhuoran
opened
6 months ago
2
Is there any parameter to set the maximum number of threads used?
#47
kuangzhuoran
opened
6 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
7 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
7 months ago
2
Pipeline failed at last clean_chains step
#44
Alchimic007
opened
8 months ago
5
Partial Lastz Process Timeouts in make_lastz_chains
#43
ZhaoHang-bio
opened
8 months ago
0
Fragmented genomes
#42
giovannaVeiga
opened
8 months ago
3
Fatal non-specific error if genome names are the same as genome filenames
#41
ning-y
opened
8 months ago
1
Fix missing double-quotes giving argparse error
#40
ning-y
closed
8 months ago
1
Multiple Alignments
#39
lutfia95
opened
9 months ago
1
TODO: add param to customise queue parameter
#38
kirilenkobm
closed
9 months ago
1
Fixing issue #35 + some additional changes - see changelog
#37
kirilenkobm
closed
9 months ago
0
issue in the lastz step
#36
lnyawen
closed
9 months ago
8
Argument list too long - lastz
#35
AgustoLuz
closed
6 months ago
8
Issue Running make_lastz_chains-2.0.6 on Test Data
#34
ZhaoHang-bio
closed
10 months ago
7
TODO? QC/statistics module
#33
kirilenkobm
opened
10 months ago
0
The pipeline does not work with 2bit files as input
#32
kirilenkobm
closed
10 months ago
1
self chains
#31
BoBo2021jenny
opened
10 months ago
2
All temp files are regulated
#30
kirilenkobm
closed
10 months ago
0
Fixed partitioning
#29
kirilenkobm
closed
10 months ago
0
Full scale run creates too many lastz jobs
#28
kirilenkobm
closed
10 months ago
1
Rearrangement
#27
kirilenkobm
closed
10 months ago
0
Uncaught exception from user code: Command failed.
#26
igorpop0v
closed
10 months ago
10
Error running make_lastz_chains on Slurm cluster
#25
philge
closed
11 months ago
6
requirements
#24
ebioman
closed
10 months ago
1
nextflow
#23
BoBo2021jenny
closed
10 months ago
1
RepeatFiller
#22
Sandhyash
closed
10 months ago
1
Error in 'lastz'
#21
hongbingp
closed
1 year ago
12
The issue with the temporary file generation path.
#20
hcsun1
closed
10 months ago
1
alignment is taking too long
#19
gunjanpandey
closed
10 months ago
4
NOTE: Process `execute_jobs (64)` terminated with an error exit status (2) -- Execution is retried (1)
#18
gunjanpandey
closed
10 months ago
3
Stalled at doPartition
#17
chenyangkang
closed
1 year ago
1
error in the step 'lastz
#16
DiegoSafian
closed
10 months ago
4
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