fix star sort memory bug

fei0810 · Aug 22, 2021 · a575c29 · a575c29
1 parent c53973c
commit a575c29
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Showing 8 changed files with 19 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -45,9 +45,9 @@ You can also use [Triti-Map](https://hub.docker.com/r/fei0810/tritimap) via Dock
 
 ```sh
 # docker pull command
-docker pull fei0810/tritimap:v0.9.6
+docker pull fei0810/tritimap:v0.9.7
 # run docker
-docker run -i -t fei0810/tritimap:v0.9.6 /bin/bash
+docker run -i -t fei0810/tritimap:v0.9.7 /bin/bash
 ```
 
 #### Installing from GitHub

diff --git a/docs/manual.md b/docs/manual.md
@@ -57,9 +57,9 @@ You can also use [Triti-Map](https://hub.docker.com/r/fei0810/tritimap) via Dock
 
 ```sh
 # docker pull command
-docker pull fei0810/tritimap:v0.9.6
+docker pull fei0810/tritimap:v0.9.7
 # run docker
-docker run -i -t fei0810/tritimap:v0.9.6 /bin/bash
+docker run -i -t fei0810/tritimap:v0.9.7 /bin/bash
 ```
 
 ### Installing from GitHub

diff --git a/docs/manual_zh.md b/docs/manual_zh.md
@@ -98,9 +98,9 @@ python setup.py install
 
 ```sh
 # 下载 Triti-Map
-docker pull fei0810/tritimap:v0.9.6
+docker pull fei0810/tritimap:v0.9.7
 # 运行 Docker 镜像
-docker run -i -t fei0810/tritimap:v0.9.6 /bin/bash
+docker run -i -t fei0810/tritimap:v0.9.7 /bin/bash
 ```
 
 ## 准备相关文件

diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 
 setuptools.setup(
  name="tritimap",
- version="0.9.6",
+ version="0.9.7",
  author="Fei Zhao",
  author_email="zhaofei920810@gmail.com",
  url="https://github.com/fei0810/Triti-Map",

diff --git a/tritimap/Snakefile b/tritimap/Snakefile
@@ -121,6 +121,13 @@ elif config['maxthreads'] < 10:
 else:
  exit("need set maxthreads")
 
+### max memory ####
+
+if config['memory'] <= 100:
+ star_memory = 100*1000000000
+else:
+ star_memory = config['memory']*1000000000
+
 #### GATK java parameter ####
 
 java_parameter = '--java-options "-Xmx'+str(config['memory'])+"G"+' -Djava.io.tmpdir='+dir_path+'"'

diff --git a/tritimap/__init__.py b/tritimap/__init__.py
@@ -1,5 +1,5 @@
 import os
 
-__version__ = "0.9.6"
+__version__ = "0.9.7"
 
 root_dir = os.path.dirname(os.path.abspath(__file__))
diff --git a/tritimap/config.yaml b/tritimap/config.yaml
@@ -70,7 +70,7 @@ snpindex:
 # If your chip-seq data have multiple histone modification types, option 'split' is recommended when the server memory is less than 300G.
 # merge_lib option: merge/split
 merge_lib: merge
-# the memory(G) spades software can use when assemble RNA-seq data
+# the memory(G) spades and STAR software can use when assemble and mapping RNA-seq data
 memory: 400
 # the kmer abyss software can use when assemble ChIP-seq data, 90 is recommended. No change needed!
 abyss:

diff --git a/tritimap/rules/rna_mapping.smk b/tritimap/rules/rna_mapping.smk
@@ -21,7 +21,7 @@ rule STAR1Mapping:
  --genomeDir {params.stardir} --readFilesCommand zcat \
  --readFilesIn {input} \
  --outFileNamePrefix {output.dir}/{params.bulk}_{params.bulktype} \
- --outSAMtype BAM Unsorted --limitBAMsortRAM 10000000000 > {log} 2>&1
+ --outSAMtype BAM Unsorted --limitBAMsortRAM 100000000000 > {log} 2>&1
  """
 
 rule STAR2Mapping:
@@ -31,6 +31,7 @@ rule STAR2Mapping:
  params:
  stardir = config['ref']['STARdir'],
  sharemem = "NoSharedMemory",
+ sort_mem = star_memory,
  bulk = lambda wildcards: wildcards.bulk,
  bulktype = lambda wildcards: wildcards.bulktype
  output:
@@ -45,7 +46,7 @@ rule STAR2Mapping:
  --genomeDir {params.stardir} --readFilesCommand zcat \
  --readFilesIn {input.fq} \
  --outFileNamePrefix {output.dir}/{params.bulk}_{params.bulktype} \
- --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 \
+ --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM {params.sort_mem} \
  --sjdbFileChrStartEnd {input.sj} \
  --outReadsUnmapped Fastx > {log} 2>&1 ;
  samtools index -c {output.step2bam}