Skip to content

Commit 2ac5a28

Browse files
committed
update splice hadnling
1 parent 681b6fb commit 2ac5a28

2 files changed

Lines changed: 8 additions & 10 deletions

File tree

FastOMA.nf

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ params.genetrees_folder = params.output_folder + "/genetrees"
1616

1717
process omamer_run{
1818
time {1.h}
19-
memory {90.GB}
19+
memory {40.GB}
2020
publishDir params.hogmap_folder
2121
input:
2222
path proteomes_omamerdb_inputhog
@@ -29,7 +29,7 @@ process omamer_run{
2929
then
3030
cp ${proteomes_omamerdb_inputhog[2]}/${proteomes_omamerdb_inputhog[0]}.hogmap ${proteomes_omamerdb_inputhog[0]}.hogmap
3131
else
32-
omamer search --db ${proteomes_omamerdb_inputhog[1]} --query ${proteomes_omamerdb_inputhog[0]} --out ${proteomes_omamerdb_inputhog[0]}.hogmap
32+
omamer search -n 10 --db ${proteomes_omamerdb_inputhog[1]} --query ${proteomes_omamerdb_inputhog[0]} --out ${proteomes_omamerdb_inputhog[0]}.hogmap
3333
fi
3434
""" // --nthreads 10
3535
}
@@ -70,7 +70,7 @@ process hog_big{
7070
publishDir params.pickles_temp
7171
cpus 6
7272
time {60.h} // for very big rhog it might need more, or you could re-run and add `-resume`
73-
memory {80.GB}
73+
memory {50.GB}
7474
input:
7575
val rhogsbig_tree_ready
7676
output:
@@ -101,7 +101,7 @@ process hog_rest{
101101

102102

103103
process collect_subhogs{
104-
memory {200.GB}
104+
memory {150.GB}
105105
publishDir params.output_folder, mode: 'copy'
106106
input:
107107
val ready_hog_rest

README.md

Lines changed: 4 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2,16 +2,14 @@ FastOMA
22
======
33
FastOMA is a scalable software package to infer orthology relationship.
44

5-
6-
75
# Input and Output:
86

97
### Input:
108
1- Sets of protein sequences in FASTA format (with `.fa` extension) in the folder `proteome`.
119
The name of each fasta file is the name of species. Please make sure that the name of fasta records do not contain `||`.
1210

1311

14-
2- The omamer database which you can download [this](https://omabrowser.org/All/LUCA.h5)
12+
2- The omamer database which you can download [this](https://omabrowser.org/All/LUCA-v2.0.0.h5)
1513
which is from [OMA browser](https://omabrowser.org/oma/current/).
1614
This file is `13 Gb` containing all the gene families of the Tree of Life or you can download it for a subset of them, e.g. Primates (352MB).
1715

@@ -110,10 +108,10 @@ If you face any difficulty during installation, feel free to create a [github is
110108
Then, cd to the `testdata` folder and download the omamer database and change its name to `omamerdb.h5`.
111109
```
112110
cd FastOMA/testdata
113-
wget https://omabrowser.org/All/Primates.h5 # 352MB
111+
wget https://omabrowser.org/All/Primates-v2.0.0.h5 # 105MB
114112
mv Primates.h5 in_folder/omamerdb.h5
115113
```
116-
(This is for the test however, I would suggest downloading the `LUCA.h5` instead of `Primates.h5` for your real analysis.). Check the item 2 in the [input section](https://github.com/sinamajidian/FastOMA#input) for details.
114+
(This is for the test however, I would suggest downloading the `LUCA-v2.0.0.h5` instead of `Primates-v2.0.0.h5` for your real analysis.). Check the item 2 in the [input section](https://github.com/sinamajidian/FastOMA#input) for details.
117115

118116
Now we have such a structure in our testdata folder.
119117
```
@@ -265,7 +263,7 @@ HUMAN00034;HUMAN00035
265263
- phylostragraphy
266264

267265
## Change log
268-
- Update v0.1.2: improve rootHOG inference, splice
266+
- Update v0.1.2: improve rootHOG inference, splice, OMAmerv2 with multi-hits
269267
- Release v0.1.0: improve nextflow pipeline and outputs.
270268
- prelease v.0.0.6: use `--fragment-detection` for `infer-subhogs` and `--low-so-detection --fragment-detection`
271269
- prelease v.0.0.6: using input hogmpa

0 commit comments

Comments
 (0)