BATCHSIZE = 25M

qiita-spots · Sep 11, 2024 · 3086bc7 · 3086bc7
1 parent 143e71f
commit 3086bc7
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/qp_woltka/tests/test_woltka.py b/qp_woltka/tests/test_woltka.py
@@ -147,16 +147,16 @@ def test_woltka_to_array_rep82(self):
             f'output={out_dir}\n',
             'bt2_cores=6\n',
             f'mxdx mux --file-map {out_dir}/files_list.tsv --batch '
-            '${SLURM_ARRAY_TASK_ID} --batch-size 600000 '
+            '${SLURM_ARRAY_TASK_ID} --batch-size 25000000 '
             '--paired-handling interleave | '
             'bowtie2 -p ${bt2_cores} -x '
             f'{database} --interleaved - --seed 42 --very-sensitive -k 16 '
             '--np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" '
             '--score-min "L,0,-0.05" --no-head --no-unal --no-exact-upfront '
             "--no-1mm-upfront | cut -f1-9 | sed \'s/$/\t*\t*/' | mxdx demux "
             f'--file-map {out_dir}/files_list.tsv '
-            '--batch ${SLURM_ARRAY_TASK_ID} --batch-size 600000 --output-base '
-            f'{out_dir}/alignments --extension sam.xz\n',
+            '--batch ${SLURM_ARRAY_TASK_ID} --batch-size 25000000 '
+            f'--output-base {out_dir}/alignments --extension sam.xz\n',
             'date\n']
         self.assertEqual(main, exp_main)
 
@@ -266,16 +266,16 @@ def test_woltka_to_array_wol(self):
             f'output={out_dir}\n',
             'bt2_cores=6\n',
             f'mxdx mux --file-map {out_dir}/files_list.tsv --batch '
-            '${SLURM_ARRAY_TASK_ID} --batch-size 600000 '
+            '${SLURM_ARRAY_TASK_ID} --batch-size 25000000 '
             '--paired-handling interleave | '
             'bowtie2 -p ${bt2_cores} -x '
             f'{database} --interleaved - --seed 42 --very-sensitive -k 16 '
             '--np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" '
             '--score-min "L,0,-0.05" --no-head --no-unal --no-exact-upfront '
             "--no-1mm-upfront | cut -f1-9 | sed \'s/$/\t*\t*/' | mxdx demux "
             f'--file-map {out_dir}/files_list.tsv '
-            '--batch ${SLURM_ARRAY_TASK_ID} --batch-size 600000 --output-base '
-            f'{out_dir}/alignments --extension sam.xz\n',
+            '--batch ${SLURM_ARRAY_TASK_ID} --batch-size 25000000 '
+            f'--output-base {out_dir}/alignments --extension sam.xz\n',
             'date\n']
         self.assertEqual(main, exp_main)
 

diff --git a/qp_woltka/woltka.py b/qp_woltka/woltka.py
@@ -33,7 +33,7 @@
 MERGE_MEMORY = '140g'
 SYNDNA_MEMORY = '190g'
 # setting so an iSeq run, generates 2 jobs
-BATCHSIZE = 600000
+BATCHSIZE = 25000000
 
 WALLTIME = '40:00:00'
 MERGE_WALLTIME = '30:00:00'