apetkau orthomcl-pipeline issues

apetkau / orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/

80 stars 36 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

=Stage 6: Split Fasta= no fasta records identified, exiting.

#51 mengmm777 opened 1 month ago
2
failing tests with t/test_pipeline.pl

#50 ccodojunior opened 3 months ago
0
Stage 5: Filter Fasta error In Window11/Ubuntu22.02.4

#49 tianyuanqihe closed 6 months ago
0
error in step 8: orthomclBlastParser blastresult compliantFasta > similarSequences.txt

#48 lyn320 closed 2 years ago
2
Stage 5: Filter Fasta error

#47 karimi81 opened 2 years ago
1
Conda installation

#46 ardy20 opened 2 years ago
1
Multiple species

#45 ardy20 opened 2 years ago
2
Stopped @ stage 8 BLAST4

#44 anu24s opened 3 years ago
1
error at Stage 10: Load Blast Results

#43 ggoodstudydaydayup opened 4 years ago
2
failing tests with t/test.pipeline.pl

#42 ggoodstudydaydayup closed 4 years ago
2
Error executing

#41 ucassee opened 4 years ago
2
The network links of virtual machine containing the OrthoMCL pipeline is broken.

#40 Caizhaohui closed 4 years ago
1
failing tests with t/test.pipeline.pl

#39 huiyus16 opened 4 years ago
2
The total number of locks exceeds the lock table size at /software/orthomclSoftware-v2.0.9/bin/orthomclPairs line 70

#38 wuxiaopei0509 closed 4 years ago
5
containing non-protein alphabet (dna)

#37 U201412486 closed 4 years ago
9
Warning: some tables exist already in database dbi:mysql:wuorthomcl:localhost:mysql_local_infile, user=liu, database_name=orthomcl. Do you want to remove (y/n)?

#36 wuxiaopei0509 closed 4 years ago
7
Questions about OrthoMCL software

#35 lanlan0210 closed 4 years ago
1
how to understand the groups.txt file

#34 U201412486 closed 4 years ago
2
error at Stage 10: Load Blast Results

#33 U201412486 closed 4 years ago
3
error at orthomcl-setup-database step

#32 naktang closed 4 years ago
3
orthomclpairs table lock size error

#31 tuguangxian closed 4 years ago
5
Set alphabet to protein

#30 apetkau closed 5 years ago
0
Is there a problem with my input file?

#29 jingydz closed 5 years ago
5
Does the MySQL version have an impact on the results?

#28 jingydz closed 5 years ago
5
Re-run orthoMCL-pipeline from a given stage ?

#27 BiodivGenomic closed 5 years ago
2
Error in test, step 3

#26 jsoghigian closed 5 years ago
2
=Stage 5: Filter Fasta= error

#25 gumingjian1 closed 5 years ago
5
=Stage 1: Validate Files =

#24 gumingjian1 closed 5 years ago
4
which MySQL version is appropriate

#23 mayupsc closed 5 years ago
2
How to continue when the orthomcl-pipeline breaked in one step?

#22 wangzhennan14 closed 5 years ago
2
where can i found the core gene set?

#21 wenjingcui closed 5 years ago
1
groups datafile further analysis

#20 wenjingcui closed 5 years ago
5
error in setp 10 when i run the orthomcl-pipeline with sge scheduler

#19 fyymxb closed 6 years ago
2
Can't set up a new mysql user count

#18 xiao7462 closed 5 years ago
1
DBD::mysql::st execute failed: Error on rename of './orthomcl/#sql-616f_3e660.MYI' to './orthomcl/SimilarSequencess.MYI' (Errcode: 2)

#17 tiramisutes closed 6 years ago
5
YAML/Tiny.pm preventing set-up

#16 abbyhudak closed 6 years ago
6
MSG: The sequence does not appear to be FASTA format (lacks a descriptor line '>')

#15 wangzhennan14 closed 6 years ago
2
Error while connection with db

#14 shrutidabral closed 6 years ago
14
Suggestion : Update to use blast+

#13 michoug closed 6 years ago
1
slurm support

#12 jos4uke closed 7 years ago
2
improvement: restart from specific step in case the pipeline stopped prematurely

#11 lassancejm closed 7 years ago
1
Fixed issue for Odd number of elements in hash assignment

#10 apetkau closed 8 years ago
0
Wrong syntax in scripts/orthomcl-pipeline.pl at line 294.

#9 ghost closed 8 years ago
1
Development

#8 apetkau closed 8 years ago
0
failing tests with t/test_pipeline.pl

#7 zmahiri closed 8 years ago
16
Development

#6 apetkau closed 9 years ago
0
add GRANT CREATE VIEW to setup step

#5 JenCabral closed 9 years ago
2
Verify README instructions for setting up database.

#4 apetkau closed 9 years ago
1
Feature/auto delete db

#3 JenCabral closed 9 years ago
0
Adding database creation to orthomcl-setup-database

#2 JenCabral closed 9 years ago
7