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erebboaherebboah
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fix GPU bug
1 parent 7dc6944 commit b156bbd

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2 files changed

+3
-35
lines changed

2 files changed

+3
-35
lines changed

‎snakemake/Snakefile_020.smk‎

Lines changed: 2 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,6 @@ rule curl_fa:
6868
threads = 1,
6969
partition = 'standard',
7070
account = 'seyedam_lab',
71-
gres = 'gpu:0',
7271
time = '4:00:00'
7372
params:
7473
link = lambda wc: get_fa_link(wc, config),
@@ -95,7 +94,6 @@ rule fa_ref_fmt:
9594
mem_gb =16,
9695
partition = 'standard',
9796
account = 'seyedam_lab',
98-
gres = 'gpu:0',
9997
time = '1:00:00'
10098
output:
10199
fa = "ref/genomes/{genotype}.fa.gz"
@@ -112,7 +110,6 @@ rule dl:
112110
threads = 1,
113111
partition = 'standard',
114112
account = 'seyedam_lab',
115-
gres = 'gpu:0',
116113
time = '4:00:00'
117114
shell:
118115
"wget -O {output.out} {params.link}"
@@ -138,7 +135,6 @@ rule kallisto_ind:
138135
threads = 12,
139136
partition = 'highmem',
140137
account = 'seyedam_lab',
141-
gres = 'gpu:0',
142138
time = '6:00:00'
143139
conda:
144140
'envs/kb_env.yaml'
@@ -175,7 +171,6 @@ rule symlink_fastq_r1:
175171
threads = 1,
176172
partition = 'standard',
177173
account = 'seyedam_lab',
178-
gres = 'gpu:0',
179174
time = '1:00:00'
180175
output:
181176
fastq = config['raw']['fastq_r1']
@@ -192,7 +187,6 @@ rule symlink_fastq_r2:
192187
threads = 1,
193188
partition = 'standard',
194189
account = 'seyedam_lab',
195-
gres = 'gpu:0',
196190
time = '1:00:00'
197191
output:
198192
fastq = config['raw']['fastq_r2']
@@ -222,7 +216,6 @@ rule kallisto:
222216
threads = 12,
223217
partition = 'highmem',
224218
account = 'seyedam_lab',
225-
gres = 'gpu:0',
226219
time = '6:00:00'
227220
output:
228221
config['kallisto']['cgb'],
@@ -261,7 +254,6 @@ rule make_unfilt_adata:
261254
threads = 4,
262255
partition = 'highmem',
263256
account = 'seyedam_lab',
264-
gres = 'gpu:0',
265257
time = '2:00:00'
266258
input:
267259
mtx = config['kallisto']['mtx'],
@@ -312,7 +304,6 @@ rule klue_fa:
312304
mem_gb = 128,
313305
partition = 'highmem',
314306
account = 'seyedam_lab',
315-
gres = 'gpu:0',
316307
time = '4:00:00'
317308
output:
318309
fa = config['ref']['klue']['fa'],
@@ -341,7 +332,6 @@ rule klue_ind:
341332
mem_gb = 128,
342333
partition = 'highmem',
343334
account = 'seyedam_lab',
344-
gres = 'gpu:0',
345335
time = '4:00:00'
346336
output:
347337
ind = config['ref']['klue']['ind']
@@ -370,7 +360,6 @@ rule klue:
370360
threads = 24,
371361
partition = 'highmem',
372362
account = 'seyedam_lab',
373-
gres = 'gpu:0',
374363
time = '6:00:00'
375364
conda:
376365
'envs/kb_env.yaml'
@@ -410,7 +399,6 @@ rule make_adata_klue:
410399
threads = 4,
411400
partition = 'highmem',
412401
account = 'seyedam_lab',
413-
gres = 'gpu:0',
414402
time = '1:00:00'
415403
input:
416404
mtx = config['klue']['mtx'],
@@ -440,7 +428,6 @@ rule klue_get_genotype_counts:
440428
threads = 2,
441429
partition = 'standard',
442430
account = 'seyedam_lab',
443-
gres = 'gpu:0',
444431
time = '1:00:00'
445432
output:
446433
ofile = config['klue']['genotype_counts']
@@ -463,8 +450,8 @@ rule cellbender:
463450
mem_gb = 128,
464451
threads = 8,
465452
partition = 'free-gpu', #'gpu'
466-
account = 'seyedam_lab',
467-
gres = 'gpu:1',
453+
account = 'seyedam_lab_gpu',
454+
gres = ' --gres=gpu:1',
468455
time = '8:00:00'
469456
output:
470457
filt_h5 = config['cellbender']['filt_h5'],
@@ -506,7 +493,6 @@ rule copy_cellbender_metrics:
506493
threads = 1,
507494
partition = 'standard',
508495
account = 'seyedam_lab',
509-
gres = 'gpu:0',
510496
time = '1:00:00'
511497
output:
512498
metrics_copy = config['cellbender']['metrics_copy']
@@ -527,7 +513,6 @@ rule make_filt_adata:
527513
threads = 4,
528514
partition = 'highmem',
529515
account = 'seyedam_lab',
530-
gres = 'gpu:0',
531516
time = '1:00:00'
532517
input:
533518
filt_h5 = config['cellbender']['filt_h5'],
@@ -558,7 +543,6 @@ rule make_tissue_adata:
558543
threads = 2,
559544
partition = 'highmem',
560545
account = 'seyedam_lab',
561-
gres = 'gpu:0',
562546
time = '2:00:00'
563547
output:
564548
adata = config['tissue']['adata']

‎snakemake/Snakefile_021.smk‎

Lines changed: 1 addition & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,6 @@ rule curl_fa:
6868
threads = 1,
6969
partition = 'standard',
7070
account = 'seyedam_lab',
71-
gres = 'gpu:0',
7271
time = '4:00:00'
7372
params:
7473
link = lambda wc: get_fa_link(wc, config),
@@ -95,7 +94,6 @@ rule fa_ref_fmt:
9594
mem_gb =16,
9695
partition = 'standard',
9796
account = 'seyedam_lab',
98-
gres = 'gpu:0',
9997
time = '1:00:00'
10098
output:
10199
fa = "ref/genomes/{genotype}.fa.gz"
@@ -112,7 +110,6 @@ rule dl:
112110
threads = 1,
113111
partition = 'standard',
114112
account = 'seyedam_lab',
115-
gres = 'gpu:0',
116113
time = '4:00:00'
117114
shell:
118115
"wget -O {output.out} {params.link}"
@@ -138,7 +135,6 @@ rule kallisto_ind:
138135
threads = 12,
139136
partition = 'highmem',
140137
account = 'seyedam_lab',
141-
gres = 'gpu:0',
142138
time = '6:00:00'
143139
conda:
144140
'envs/kb_env.yaml'
@@ -175,7 +171,6 @@ rule symlink_fastq_r1:
175171
threads = 1,
176172
partition = 'standard',
177173
account = 'seyedam_lab',
178-
gres = 'gpu:0',
179174
time = '1:00:00'
180175
output:
181176
fastq = config['raw']['fastq_r1']
@@ -192,7 +187,6 @@ rule symlink_fastq_r2:
192187
threads = 1,
193188
partition = 'standard',
194189
account = 'seyedam_lab',
195-
gres = 'gpu:0',
196190
time = '1:00:00'
197191
output:
198192
fastq = config['raw']['fastq_r2']
@@ -222,7 +216,6 @@ rule kallisto:
222216
threads = 12,
223217
partition = 'highmem',
224218
account = 'seyedam_lab',
225-
gres = 'gpu:0',
226219
time = '6:00:00'
227220
output:
228221
config['kallisto']['cgb'],
@@ -261,7 +254,6 @@ rule make_unfilt_adata:
261254
threads = 4,
262255
partition = 'highmem',
263256
account = 'seyedam_lab',
264-
gres = 'gpu:0',
265257
time = '2:00:00'
266258
input:
267259
mtx = config['kallisto']['mtx'],
@@ -312,7 +304,6 @@ rule klue_fa:
312304
mem_gb = 128,
313305
partition = 'highmem',
314306
account = 'seyedam_lab',
315-
gres = 'gpu:0',
316307
time = '4:00:00'
317308
output:
318309
fa = config['ref']['klue']['fa'],
@@ -341,7 +332,6 @@ rule klue_ind:
341332
mem_gb = 128,
342333
partition = 'highmem',
343334
account = 'seyedam_lab',
344-
gres = 'gpu:0',
345335
time = '4:00:00'
346336
output:
347337
ind = config['ref']['klue']['ind']
@@ -370,7 +360,6 @@ rule klue:
370360
threads = 24,
371361
partition = 'highmem',
372362
account = 'seyedam_lab',
373-
gres = 'gpu:0',
374363
time = '6:00:00'
375364
conda:
376365
'envs/kb_env.yaml'
@@ -410,7 +399,6 @@ rule make_adata_klue:
410399
threads = 4,
411400
partition = 'highmem',
412401
account = 'seyedam_lab',
413-
gres = 'gpu:0',
414402
time = '1:00:00'
415403
input:
416404
mtx = config['klue']['mtx'],
@@ -440,7 +428,6 @@ rule klue_get_genotype_counts:
440428
threads = 2,
441429
partition = 'standard',
442430
account = 'seyedam_lab',
443-
gres = 'gpu:0',
444431
time = '1:00:00'
445432
output:
446433
ofile = config['klue']['genotype_counts']
@@ -464,7 +451,7 @@ rule cellbender:
464451
threads = 8,
465452
partition = 'free-gpu', #'gpu'
466453
account = 'seyedam_lab_gpu',
467-
gres = 'gpu:1',
454+
gres = ' --gres=gpu:1',
468455
time = '8:00:00'
469456
output:
470457
filt_h5 = config['cellbender']['filt_h5'],
@@ -506,7 +493,6 @@ rule copy_cellbender_metrics:
506493
threads = 1,
507494
partition = 'standard',
508495
account = 'seyedam_lab',
509-
gres = 'gpu:0',
510496
time = '1:00:00'
511497
output:
512498
metrics_copy = config['cellbender']['metrics_copy']
@@ -527,7 +513,6 @@ rule make_filt_adata:
527513
threads = 4,
528514
partition = 'highmem',
529515
account = 'seyedam_lab',
530-
gres = 'gpu:0',
531516
time = '1:00:00'
532517
input:
533518
filt_h5 = config['cellbender']['filt_h5'],
@@ -558,7 +543,6 @@ rule make_tissue_adata:
558543
threads = 2,
559544
partition = 'highmem',
560545
account = 'seyedam_lab',
561-
gres = 'gpu:0',
562546
time = '2:00:00'
563547
output:
564548
adata = config['tissue']['adata']

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