gsneha26 SegAlign issues

gsneha26 / SegAlign

A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043

MIT License

66 stars 16 forks source link

issues

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SegAlign Dumps Core on Large Complex Genomes (>8Gb)

#67 DevonJBoland closed 1 month ago
2
Segmentation fault error

#66 aaannaw opened 4 months ago
0
Support for linux-ppc64le?

#65 taoqxtaozi opened 6 months ago
0
Added the ability for SegAlign to read and use a lastz scoring file.

#64 richard-burhans closed 2 months ago
0
Output file size not correct

#63 gotouerina opened 7 months ago
1
AMD GPU support

#62 fluidnumerics-joe opened 8 months ago
0
/usr/local/bin/run_segalign: line 60: segalign: command not found

#61 osyafinkelberg opened 10 months ago
1
Error: cudaMalloc of 256 bytes for sub_mat failed with error " the provided PTX was compiled with an unsupported toolchain. "

#60 gotouerina opened 1 year ago
1
thrust::system::system_error | CUDA free failed: cudaErrorCudartUnloading

#59 chenhijy opened 1 year ago
0
SegAlign crashes while running cactus on Terra

#58 hloucks opened 2 years ago
3
run_segalign crashes on human-chimp (and exits 0!)

#57 glennhickey opened 2 years ago
2
segalign crashes while aligning final against final reference block

#56 spo-colossal opened 2 years ago
1
Sync with Cactus

#55 glennhickey opened 2 years ago
0
segaling_repeat_masker still crashes

#54 glennhickey opened 2 years ago
7
segalign_repeat_masker crashes

#53 glennhickey closed 2 years ago
3
error during cmake

#52 michaelgelliot closed 2 years ago
1
stdbuf: failed to run command ‘segalign’: No such file or directory

#51 mdsufz closed 2 years ago
2
cudaErrorIllegalAddress: an illegal memory access was encountered

#50 tothuhien closed 2 years ago
1
run_segalign_repeat_masker file

#49 estolle closed 3 years ago
2
SegAlign/progressivecactus errors on LSF

#48 fabrimafe closed 3 years ago
1
FAILURE: extra segments in file

#47 glennhickey closed 3 years ago
4
"grep: *.err" and "m: cannot remove '*.segments'" errors

#46 thiagogenez closed 3 years ago
2
Running on multi-fasta

#45 niederhuth closed 3 years ago
2
couldn't find boost

#44 zhenzhenyang-psu closed 3 years ago
7
Post process dev

#43 gsneha26 closed 4 years ago
0
segalign_repeat_masker runs out of memory on kangaroo rat

#42 glennhickey closed 4 years ago
2
Updating before combine

#41 gsneha26 closed 4 years ago
0
Fix Sort

#40 glennhickey closed 4 years ago
0
Error in LASTZ process!

#39 glennhickey closed 4 years ago
1
Erase tmp files as they are output to save space

#38 glennhickey closed 4 years ago
7
run_segalign_repeat_masker can fail without error code

#37 glennhickey closed 4 years ago
1
run_segalign_repeat_masker doesn't appear to work

#36 glennhickey closed 4 years ago
4
Merge pull request #34 from gsneha26/master

#35 gsneha26 closed 4 years ago
0
Merge

#34 gsneha26 closed 4 years ago
0
Added build workflow in Travis CI and added corresponding badge

#33 gsneha26 closed 4 years ago
0
Combined repeat mask

#32 gsneha26 closed 4 years ago
0
Repeat mask

#31 gsneha26 closed 4 years ago
0
Emr cluster dev

#30 gsneha26 closed 4 years ago
0
add back support for special chars in fasta sequence names

#29 gsneha26 closed 4 years ago
0
Still worried about exit codes

#28 glennhickey closed 4 years ago
3
Human/Chimp stats

#27 glennhickey closed 4 years ago
1
Use loop when deleting files instead of passing wildcards to rm

#26 glennhickey closed 4 years ago
0
Special characters no longer supported

#25 glennhickey closed 4 years ago
4
Bash error in run_wga_gpu

#24 glennhickey closed 4 years ago
1
Add back support for special chars in fasta sequence names

#23 glennhickey closed 4 years ago
1
Add Dockerfile

#22 glennhickey closed 4 years ago
0
right extension issue

#21 gsneha26 closed 4 years ago
0
Limit number of lastz processes from run_wga_gpu

#20 yatisht closed 4 years ago
0
Please add system requirements and limits to README

#19 glennhickey closed 4 years ago
0
run_wga_gpu crashes on all-against-all human chimp alignment

#18 glennhickey closed 4 years ago
2