利用老师课程中讲的方法一pick_de_novo_otus.py进行的，但运行过程的日志文件中出现assign_taxonomy过程的报错。
[root@f0190be56047 21:19:38 /work/my_16s/5.pick_otu_qiime]# pick_de_novo_otus.py -i qiime.fasta -f -o pick_de_novo_otus \
> -p otu_params_de_novo.txt
Traceback (most recent call last):
File "/biosoft/miniconda/envs/qiime1/bin/pick_de_novo_otus.py", line 180, in <module>
main()
File "/biosoft/miniconda/envs/qiime1/bin/pick_de_novo_otus.py", line 177, in main
status_update_callback=status_update_callback)
File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/upstream.py", line 306, in run_pick_de_novo_otus
close_logger_on_success=close_logger_on_success)
File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Assign taxonomy
Command run was:
assign_taxonomy.py -o pick_de_novo_otus/uclust_assigned_taxonomy -i pick_de_novo_otus/rep_set//qiime_rep_set.fasta --reference_seqs_fp /work/database/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/97/silva_132_97_16S.fna --id_to_taxonomy_fp /work/database/SILVA_132_QIIME_release/taxonomy/16S_only/97/taxonomy_7_levels.txt --assignment_method uclust --similarity 0.8
Command returned exit status: 1
Stdout:
Stderr
sh: line 1: 1085 Killed uclust --input "pick_de_novo_otus/rep_set//qiime_rep_set.fasta" --id 0.8 --rev --maxaccepts 3 --allhits --libonly --lib "/work/database/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/97/silva_132_97_16S.fna" --uc "/work/tmp/UclustConsensusTaxonAssigner_2xGIhB.uc" > "/work/tmp/tmpVz73v6rkGDHP8P6Dl7vq.txt" 2> "/work/tmp/tmp65PbAsdasr2UqVI3AjB2.txt"
Traceback (most recent call last):
File "/biosoft/miniconda/envs/qiime1/bin/assign_taxonomy.py", line 417, in <module>
main()
File "/biosoft/miniconda/envs/qiime1/bin/assign_taxonomy.py", line 394, in main
log_path=log_path)
File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 1304, in __call__
'--uc': uc_path})
File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/burrito/util.py", line 285, in __call__
'StdErr:\n%s\n' % open(errfile).read())
burrito.util.ApplicationError: Unacceptable application exit status: 137
Command:
cd "/work/my_16s/5.pick_otu_qiime/"; uclust --input "pick_de_novo_otus/rep_set//qiime_rep_set.fasta" --id 0.8 --rev --maxaccepts 3 --allhits --libonly --lib "/work/database/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/97/silva_132_97_16S.fna" --uc "/work/tmp/UclustConsensusTaxonAssigner_2xGIhB.uc" > "/work/tmp/tmpVz73v6rkGDHP8P6Dl7vq.txt" 2> "/work/tmp/tmp65PbAsdasr2UqVI3AjB2.txt"
StdOut:
StdErr:
uclust v1.2.22q
(C) Copyright 2009-10 Robert C. Edgar
Licensed ONLY for use in PyNAST and QIIME.
00:00 37Mb 0.0% Reading lib, 0 seeds
00:01 74Mb 0.6% Reading lib, 788 seeds
00:02 306Mb 4.2% Reading lib, 6577 seeds
00:03 519Mb 7.5% Reading lib, 11845 seeds
00:04 742Mb 11.0% Reading lib, 17427 seeds
00:05 909Mb 13.6% Reading lib, 21646 seeds
00:06 1.0Gb 15.5% Reading lib, 24715 seeds
00:07 1.2Gb 18.0% Reading lib, 28768 seeds
00:08 1.4Gb 20.5% Reading lib, 32852 seeds
00:09 1.5Gb 23.3% Reading lib, 37364 seeds
00:10 1.7Gb 26.0% Reading lib, 41888 seeds
00:11 1.8Gb 28.0% Reading lib, 45100 seeds
00:12 2.0Gb 30.9% Reading lib, 49940 seeds
00:13 2.2Gb 33.8% Reading lib, 54647 seeds
00:14 2.4Gb 36.2% Reading lib, 58565 seeds
00:15 2.6Gb 38.8% Reading lib, 62941 seeds
00:16 2.7Gb 41.1% Reading lib, 66756 seeds
00:17 2.9Gb 43.5% Reading lib, 70754 seeds
00:18 3.0Gb 46.5% Reading lib, 75884 seeds
00:19 3.2Gb 48.6% Reading lib, 79287 seeds
00:20 3.4Gb 51.1% Reading lib, 83608 seeds
00:21 3.6Gb 54.0% Reading lib, 88492 seeds
00:22 3.7Gb 56.9% Reading lib, 93383 seeds
00:23 3.9Gb 59.8% Reading lib, 98460 seeds
00:24 4.1Gb 62.0% Reading lib, 102153 seeds
00:25 4.2Gb 64.3% Reading lib, 106175 seeds
00:26 4.3Gb 66.6% Reading lib, 110147 seeds
00:27 4.4Gb 68.1% Reading lib, 112832 seeds
00:28 4.6Gb 69.8% Reading lib, 115858 seeds
00:29 4.6Gb 71.3% Reading lib, 118395 seeds
00:30 4.7Gb 72.9% Reading lib, 121208 seeds
00:31 4.8Gb 74.3% Reading lib, 123781 seeds
00:32 4.9Gb 75.1% Reading lib, 125206 seeds
00:33 5.0Gb 76.3% Reading lib, 127223 seeds
00:34 5.1Gb 77.5% Reading lib, 129335 seeds
00:35 5.1Gb 78.5% Reading lib, 131110 seeds
00:36 5.2Gb 79.6% Reading lib, 133140 seeds
00:37 5.3Gb 80.8% Reading lib, 135267 seeds
00:38 5.3Gb 81.6% Reading lib, 136757 seeds
00:39 5.5Gb 83.2% Reading lib, 139515 seeds
00:40 5.5Gb 83.2% Reading lib, 139630 seeds
00:41 5.5Gb 84.2% Reading lib, 141336 seeds
00:42 5.5Gb 84.3% Reading lib, 141613 seeds
用的ampliseq-q1:v1.2的版本
