老师你好,我在使用qiime进行聚类分析中的pick_open_reference_otus.py进行聚类时,总是提示usearch61的版本不对,后来使用psortmerna_sumaclust 分析到一半的时候也开始报错了

具体报错的信息如下

Traceback (most recent call last):

  File "/biosoft/miniconda/envs/qiime1/bin/pick_open_reference_otus.py", line 453, in <module>

    main()

  File "/biosoft/miniconda/envs/qiime1/bin/pick_open_reference_otus.py", line 432, in main

    minimum_failure_threshold=minimum_failure_threshold)

  File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 1030, in pick_subsampled_open_reference_otus

    status_update_callback=status_update_callback)

  File "/biosoft/miniconda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 232, in assign_tax

    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_open_reference_otus/uclust_assigned_taxonomy -i pick_open_reference_otus/rep_set.fna --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:   556 Segmentation fault      uclust --input "pick_open_reference_otus/rep_set.fna" --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_3che8T.uc" > "/work/tmp/tmpcfK94YiqcvPEpOq0MYbL.txt" 2> "/work/tmp/tmpYU1idAfaqTFEbQtQEBGJ.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: 139

Command:

cd "/work/mylunwen/5.pick_otu_qiime/"; uclust --input "pick_open_reference_otus/rep_set.fna" --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_3che8T.uc" > "/work/tmp/tmpcfK94YiqcvPEpOq0MYbL.txt" 2> "/work/tmp/tmpYU1idAfaqTFEbQtQEBGJ.txt"

StdOut:


StdErr:

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

如果用的是docker,电脑内存不够吧,https://www.omicsclass.com/article/1413


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  • ........ 提出于 2023-05-19 11:55

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