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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Raw align failed #51

Closed kinglyyang closed 4 years ago

kinglyyang commented 4 years ago

Hi Dr. Hu,

Thank you so much for your fantastic tool! I have a question when I tried to run nextdenovo. My run.cfg is like this:

[General] job_type = local job_prefix = nextD_t1 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 16 input_type = raw input_fofn = ./input.fofn workdir = ./run_t1

[correct_option] read_cutoff = 1k seed_cutoff = 8367 blocksize = 5g pa_correction = 16 seed_cutfiles = 16 sort_options = -m 5g -t 16 -k 40 minimap2_options_raw = -x ava-ont -t 16 correction_options = -p 16

[assemble_option] random_round = 20 minimap2_options_cns = -x ava-ont -t 16 -k17 -w17 nextgraph_options = -a 1

However, the work was terminated after about 3 hours of running with error message "raw align failed'. I also checked the log file in which 280 jobs were created, but 170 were failed after three times of rerunning (I guess this is related to the "rerun = 3"). It was run on cluster but I only have one node with 16 cores and 100 Gb of memory. Could you please help me find where the problem is? Thank you so much in advance!

KY

moold commented 4 years ago

Hi, could you paste the log of failed-jobs to here? BTW, why your seed_cutoff is so short and how many data you used for assembly?

kinglyyang commented 4 years ago

Thank you so much! I'm sorry the log file for the above one was carelessly removed, but we have run another job with the same problem. So I paste the cfg and log file here. The seed_cutoff was generated by seq_stat for which I also paste the log file here.

@@ run.cfg [General] job_type = local job_prefix = nextD_t1 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 20 parallel_jobs = 16 input_type = raw input_fofn = ./input.fofn workdir = ./run_t1

[correct_option] read_cutoff = 1k seed_cutoff = 8367 blocksize = 5g pa_correction = 4 seed_cutfiles = 4 sort_options = -m 5g -t 16 -k 40 minimap2_options_raw = -x ava-ont -t 16 correction_options = -p 4

[assemble_option] random_round = 20 minimap2_options_cns = -x ava-ont -t 16 -k17 -w17 nextgraph_options = -a 1

@@log file [INFO] 2020-02-10 23:40:36,947 start... [INFO] 2020-02-10 23:40:36,951 logfile: pid5802.log.info [WARNING] 2020-02-10 23:40:36,954 Re-write workdir [INFO] 2020-02-10 23:40:36,954 options: [INFO] 2020-02-10 23:40:36,954 {'sort_threads': 16, 'nodelist': '', 'rewrite': 1, 'blocksize': '5g', 'job_prefix': 'nextD_t1', 'job_type': 'local', 'minimap2_options_raw': '-x ava-ont -t 16', 'cns_threads': 4, 'sort_mem': '5g', 'seed_cutoff': '8367', 'input_fofn': '/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./input.fofn', 'read_cutoff': '1k', 'input_type': 'raw', 'sort_options': '-m 5g -t 16 -k 40', 'parallel_jobs': '16', 'cluster_options': '', 'sge_queue': '', 'ctg_graphdir': '/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/03.ctg_graph', 'pa_correction': '4', 'workdir': '/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1', 'random_round': '20', 'minimap2_threads': (16, 16), 'minimap2_options_cns': '-x ava-ont -t 16 -k17 -w17', 'cns_aligndir': '/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/02.cns_align', 'seed_cutfiles': '4', 'raw_aligndir': '/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/01.raw_align', 'task': 'all', 'deltmp': 1, 'rerun': 10, 'correction_options': '-p 4 -max_lq_length 10000', 'nextgraph_options': '-a 1'} [INFO] 2020-02-10 23:40:36,955 mkdir: /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1 [INFO] 2020-02-10 23:40:36,956 mkdir: /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/01.raw_align [INFO] 2020-02-10 23:40:36,956 mkdir: /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/02.cns_align [INFO] 2020-02-10 23:40:36,957 mkdir: /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/./run_t1/03.ctg_graph [INFO] 2020-02-10 23:40:36,959 analysis tasks done [INFO] 2020-02-10 23:40:36,962 total jobs: 1 [INFO] 2020-02-10 23:40:36,963 Throw jobID:[5806] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/01.db_split.sh.work/db_split0/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:21,927 db_split done [INFO] 2020-02-10 23:51:22,010 analysis tasks done [INFO] 2020-02-10 23:51:22,884 total jobs: 20 [INFO] 2020-02-10 23:51:22,885 Throw jobID:[7034] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align00/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:23,388 Throw jobID:[7041] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align01/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:23,890 Throw jobID:[7046] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align02/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:24,393 Throw jobID:[7051] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align03/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:24,896 Throw jobID:[7060] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align04/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:25,399 Throw jobID:[7068] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align05/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:25,902 Throw jobID:[7077] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align06/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:26,404 Throw jobID:[7085] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align07/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:26,906 Throw jobID:[7096] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align08/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:27,408 Throw jobID:[7102] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align09/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:27,911 Throw jobID:[7110] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align10/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:28,413 Throw jobID:[7119] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align11/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:28,915 Throw jobID:[7127] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align12/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:29,417 Throw jobID:[7135] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align13/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:29,919 Throw jobID:[7144] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align14/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:51:30,421 Throw jobID:[7152] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align15/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:55:18,621 Throw jobID:[7624] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align16/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:56:12,262 Throw jobID:[8098] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align17/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:56:12,792 Throw jobID:[8103] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align18/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-10 23:56:54,275 Throw jobID:[8172] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align19/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:45,583 18 raw_align jobs failed, and rerun with the 10 time [INFO] 2020-02-11 06:21:45,635 total jobs: 18 [INFO] 2020-02-11 06:21:45,636 Throw jobID:[4721] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align00/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:46,139 Throw jobID:[4726] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align02/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:46,642 Throw jobID:[4730] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align03/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:47,144 Throw jobID:[4735] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align04/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:47,647 Throw jobID:[4741] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align06/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:48,150 Throw jobID:[4750] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align07/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:48,653 Throw jobID:[4758] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align08/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:49,155 Throw jobID:[4767] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align09/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:49,658 Throw jobID:[4775] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align10/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:50,161 Throw jobID:[4784] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align11/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:50,664 Throw jobID:[4794] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align12/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:51,166 Throw jobID:[4802] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align13/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:51,668 Throw jobID:[4811] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align14/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:52,170 Throw jobID:[4819] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align15/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:52,672 Throw jobID:[4828] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align16/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:21:53,175 Throw jobID:[4836] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align17/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:24:18,348 Throw jobID:[5036] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align18/nextD_t1.sh] in the local_cycle. [INFO] 2020-02-11 06:24:18,920 Throw jobID:[5041] jobCmd:[/crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align19/nextD_t1.sh] in the local_cycle.

@@seq_stat [Read length histogram ('*' =~ 3497 reads)] 0 999 0
1000 1999 38204 ** 2000 2999 37932 ** 3000 3999 77330 ** 4000 4999 46045 * 5000 5999 64342 ** 6000 6999 62942 ***** 7000 7999 45269 **** 8000 8999 51317 ** 9000 9999 65886 ** 10000 10999 83273 * 11000 11999 101660 *** 12000 12999 119260 ** 13000 13999 133338 ** 14000 14999 144412 * 15000 15999 150635 *** 16000 16999 152574 17000 17999 151977 18000 18999 147540 ** 19000 19999 142523 **** 20000 20999 136058 ** 21000 21999 129118 **** 22000 22999 121385 ** 23000 23999 114041 **** 24000 24999 105983 ** 25000 25999 99747 **** 26000 26999 91720 ** 27000 27999 85189 **** 28000 28999 78515 ** 29000 29999 72491 **** 30000 30999 66296 ** 31000 31999 60192 ** 32000 32999 54695 33000 33999 49547 ** 34000 34999 44991 **** 35000 35999 40087 * 36000 36999 35879 **** 37000 37999 32223 * 38000 38999 28645 **** 39000 39999 25468 * 40000 40999 22784 **** 41000 41999 20125 * 42000 42999 18171 * 43000 43999 16001 ** 44000 44999 14007 *** 45000 45999 12504 46000 46999 11108 47000 47999 9774 48000 48999 8339 49000 49999 7644 50000 50999 6683 51000 51999 6074 52000 52999 5385 53000 53999 4663 54000 54999 4230 55000 55999 3780 * 56000 56999 3357
57000 57999 3095
58000 58999 2651
59000 59999 2321
60000 60999 2266
61000 61999 1929
62000 62999 1776
63000 63999 1636
64000 64999 1472
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66000 66999 1276
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139000 139999 10
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163000 163999 4
164000 164999 1
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167000 167999 3
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171000 171999 0
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173000 173999 0
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175000 175999 2
176000 176999 2
177000 177999 3
178000 178999 2
179000 179999 2
180000 180999 1
181000 181999 5
182000 182999 1
183000 183999 1
184000 184999 0
185000 185999 3
186000 186999 1
187000 187999 1
188000 188999 1
189000 189999 3
190000 190999 2
191000 191999 0
192000 192999 1
193000 193999 1
194000 194999 0
195000 195999 3
196000 196999 1
197000 197999 2
198000 198999 0
199000 199999 1
200000 200999 0
201000 201999 1
202000 202999 0
203000 203999 0
204000 204999 3
205000 205999 0
206000 206999 2
207000 207999 1
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209000 209999 1
210000 210999 0
211000 211999 1
212000 212999 0
213000 213999 0
214000 214999 1
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218000 218999 1
219000 219999 0
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223000 223999 0
224000 224999 0
225000 225999 0
226000 226999 1
227000 227999 2
228000 228999 0
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232000 232999 0
233000 233999 1
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235000 235999 0
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237000 237999 1
238000 238999 0
239000 239999 0
240000 240999 1
241000 241999 0
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243000 243999 0
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245000 245999 0
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247000 247999 0
248000 248999 0
249000 249999 0
250000 250999 0
251000 251999 0
252000 252999 0
253000 253999 0
254000 254999 1
255000 255999 1
256000 256999 0
257000 257999 0
258000 258999 0
259000 259999 0
260000 260999 0
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299000 299999 0
300000 300999 0
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[Read length stat] Types Count (#) Length (bp) N10 136666 43701 N20 324110 36190 N30 543165 31614 N40 791424 28083 N50 1070167 25046 N60 1383055 22267 N70 1736417 19608 N80 2141744 16880 N90 2625433 13604

Types Count (#) Bases (bp) Depth (X) Raw 3618147 73934814796 46.21 Filtered 120255 57842970 0.04 Clean 3497892 73876971826 46.17

*Suggested length cutoff of reads (genome size: 1600000000, expected seed depth: 45) to be corrected: 8367 bp

moold commented 4 years ago

Hi, can you paste the log of error subtasks: /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align*/nextD_t1.sh.log, not the log of main task.

kinglyyang commented 4 years ago

Thank you so much! But I just couldn't find the .log file in all the raw_align*/ folders. The files there are like: image or image

moold commented 4 years ago

nextD_t1.sh.e is the log file.

kinglyyang commented 4 years ago

Thank you so much! I pasted several log files below:

hostname

hostname

hostname

real 4m26.919s user 10m9.874s sys 1m30.499s touch /crex/proj/uppstore2017058/private/proj1-green/nanopore/assemblies/nextD_t1/run_t1/01.raw_align/02.raw_align.sh.work/raw_align16/nextD_t1.sh.done

moold commented 4 years ago

The log you pasted is a normally completed subtask, and you should paste the log of unfinished error subtasks.

kinglyyang commented 4 years ago

Thank you so much! I think the first log is an abnormal one. And I also pasted several other error ones.

hostname

hostname

hostname

hostname

moold commented 4 years ago

As the log shown, the error subtasks are killed by the system, which are usually caused by insufficent memory, see #48 for a solutation.

kinglyyang commented 4 years ago

I'll try to solve it according to your advice. Thank you so much!