- pindel back to --max_range_index 3

- gstrip_preprocess now requires 16Gb of memory

cluster.yaml

@@ -18,7 +18,7 @@ genomestrip:
   mem: 8
 
 preprocess:
-  mem: 8
+  mem: 16
   time: "72:00:00"
 
 cnvpipeline:

snakecnv/bin/gstrip_preprocess.py

@@ -40,7 +40,7 @@ def launch(bamlist, reference, gendermap, outdir, outprefix):
     old_libpath = ":" + os.environ["LD_LIBRARY_PATH"] if "LD_LIBRARY_PATH" in os.environ else ""
     os.environ["LD_LIBRARY_PATH"] = sv_dir + "/bwa" + old_libpath
 
-    mx = "-Xmx4g"
+    mx = "-Xmx16g"
     classpath = "{sv_dir}/lib/SVToolkit.jar:{sv_dir}/lib/gatk/GenomeAnalysisTK.jar:{sv_dir}/lib/gatk/Queue.jar". \
         format(sv_dir=sv_dir)
 
@@ -58,7 +58,7 @@ def launch(bamlist, reference, gendermap, outdir, outprefix):
                     .format(classpath=classpath, mx=mx, sv_dir=sv_dir), shell=True).returncode
     if exit_code != 0:
         return fail("An error has occurred. See above.")
-    
+
     command = (
         """LC_ALL=C java -cp {classpath} {mx} \
 org.broadinstitute.gatk.queue.QCommandLine \

snakecnv/tools/pindel.snk

@@ -41,10 +41,11 @@ rule pindel:
     shell:
         "pindel -f {input.genome} -i {input.statfile}"
         "       --min_perfect_match_around_BP 20 "
+        "       --max_range_index 3 "
         "       --exclude {input.excluded}"
         "       --number_of_threads {threads}"
         "       --report_interchromosomal_events false"
-        "       --window_size 1" # 1Mb
+        "       --window_size 1"  # 1Mb
         "       --minimum_support_for_event 3 -c {wildcards.chrom}:{wildcards.chrbatch}"
         "       -o {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}"
         "       1>{log.stdout} 2>{log.stderr}"