wangyibin
ERROR Couldn't run first cluster.
您好！我们最近在用你们的软件进行组装具体参数如下
cphasing pipeline -f asm.hic.p_utg.fa -hic1 fastq/merge_R1.fastq.gz -hic2 fastq/merge_R1.fastq.gz -t 10 -n 0:0 -hic-mapper-k 27 -hic-mapper-w 14
在聚类的时候报了如下错误：
ERROR Couldn't run first cluster. cli.py:1180
╭───── Traceback (most recent call last) ──────╮
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/cli.py:1113 in pipeline │
│ │
│ 1110 │ │
│ 1111 │ today = datetime.now().strftime(" │
│ 1112 │ try: │
│ ❱ 1113 │ │ run(fasta, │
│ 1114 │ │ │ ul_data, │
│ 1115 │ │ │ porec_data, │
│ 1116 │ │ │ porectable, pairs, │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/pipeline/pipeline.py:1061 in run │
│ │
│ 1058 │ │ │ out_sh.write("\n") │
│ 1059 │ │ │
│ 1060 │ │ try: │
│ ❱ 1061 │ │ │ hyperpartition.main(args= │
│ 1062 │ │ │ │ │ │ │ prog_name │
│ 1063 │ │ except SystemExit as e: │
│ 1064 │ │ │ exc_info = sys.exc_info() │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/ri │
│ ch_click/rich_command.py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(c │
│ 127 │ │ │ │ │ if not standalone │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:1443 in invoke │
│ │
│ 1440 │ │ │ echo(style(message, fg="r │
│ 1441 │ │ │
│ 1442 │ │ if self.callback is not None: │
│ ❱ 1443 │ │ │ return ctx.invoke(self.ca │
│ 1444 │ │
│ 1445 │ def shell_complete(self, ctx: Con │
│ 1446 │ │ """Return a list of completio │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:788 in invoke │
│ │
│ 785 │ │ │
│ 786 │ │ with augment_usage_errors(__s │
│ 787 │ │ │ with ctx: │
│ ❱ 788 │ │ │ │ return __callback(*ar │
│ 789 │ │
│ 790 │ def forward(__self, _cmd: "Comma │
│ 791 │ │ """Similar to :meth:invoke │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/cli.py:4126 in hyperpartition │
│ │
│ 4123 │ │ │ sys.exit(-1) │
│ 4124 │ │ │ hp.phased_merge_cluster( │
│ 4125 │ │ else: │
│ ❱ 4126 │ │ │ hp.incremental_partition( │
│ 4127 │ else: │
│ 4128 │ │ if merge_cluster: │
│ 4129 │ │ │ groups = list(_merge_clus │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/hyperpartition.py:1068 in │
│ incremental_partition │
│ │
│ 1065 │ │ │ │ │
│ 1066 │ │ │ │ self.K = list(filter( │
│ 1067 │ │ │ │
│ ❱ 1068 │ │ │ assert len(self.K) > 0, " │
│ 1069 │ │ │ self.to_cluster(f'first.c │
│ 1070 │ │ │ first_cluster_file = f'fi │
│ 1071 │
╰──────────────────────────────────────────────╯
AssertionError: Couldn't run first cluster.
请帮忙看看是什么导致的？谢谢
你好，不好意思，这是我们编辑文档的时候编辑错了。 应该改成分别输入Hi-C数据的R1和R2：
cphasing pipeline -f asm.hic.p_utg.fa -hic1 fastq/merge_R1.fastq.gz -hic2 fastq/merge_R2.fastq.gz -t 10 -n 0:0 -hic-mapper-k 27 -hic-mapper-w 14
你好，不好意思，这是我们编辑文档的时候编辑错了。 应该改成分别输入Hi-C数据的R1和R2：
cphasing pipeline -f asm.hic.p_utg.fa -hic1 fastq/merge_R1.fastq.gz -hic2 fastq/merge_R2.fastq.gz -t 10 -n 0:0 -hic-mapper-k 27 -hic-mapper-w 14
好的，谢谢
[09:03:23] ERROR Duplicate key "Chr01g3" cli.py:1180 RemoteTraceback: """ Traceback (most recent call last): File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/joblib/ex ternals/loky/process_executor.py", line 463, in process_worker r = call_item() ^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/joblib/ex ternals/loky/process_executor.py", line 291, in call return self.fn(*self.args, **self.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/joblib/pa rallel.py", line 598, in call return [func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/cphasing/ cli.py", line 2664, in func pa.run() File "/public/home/lgl_xy/software/CPhasing/cphasing/ alleles.py", line 368, in run self.is_split = self.split_contig() ^^^^^^^^^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/cphasing/ alleles.py", line 267, in split_contig contigsize = get_contig_length(self.fasta) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/cphasing/ utilities.py", line 583, in get_contig_length fasta = Fasta(fasta) ^^^^^^^^^^^^ File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/pyfaidx/ init.py", line 1090, in init self.faidx = Faidx( ^^^^^^ File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/pyfaidx/_ init_.py", line 511, in init self.read_fai() File "/public/home/lgl_xy/software/CPhasing/.pixi/env s/default/lib/python3.12/site-packages/pyfaidx/_ init_.py", line 567, in read_fai raise ValueError('Duplicate key "%s"' % key) ValueError: Duplicate key "Chr01g3" """
The above exception was the direct cause of the
following exception:
╭───── Traceback (most recent call last) ──────╮
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/cli.py:1113 in pipeline │
│ │
│ 1110 │ │
│ 1111 │ today = datetime.now().strftime(" │
│ 1112 │ try: │
│ ❱ 1113 │ │ run(fasta, │
│ 1114 │ │ │ ul_data, │
│ 1115 │ │ │ porec_data, │
│ 1116 │ │ │ porectable, pairs, │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/pipeline/pipeline.py:1061 in run │
│ │
│ 1058 │ │ │ _out_sh.write("\n") │
│ 1059 │ │ │
│ 1060 │ │ try: │
│ ❱ 1061 │ │ │ hyperpartition.main(args= │
│ 1062 │ │ │ │ │ │ │ prog_name │
│ 1063 │ │ except SystemExit as e: │
│ 1064 │ │ │ exc_info = sys.exc_info() │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/ri │
│ ch_click/rich_command.py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(c │
│ 127 │ │ │ │ │ if not standalone_ │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:1443 in invoke │
│ │
│ 1440 │ │ │ echo(style(message, fg="r │
│ 1441 │ │ │
│ 1442 │ │ if self.callback is not None: │
│ ❱ 1443 │ │ │ return ctx.invoke(self.ca │
│ 1444 │ │
│ 1445 │ def shell_complete(self, ctx: Con │
│ 1446 │ │ """Return a list of completio │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:788 in invoke │
│ │
│ 785 │ │ │
│ 786 │ │ with augment_usage_errors(__s │
│ 787 │ │ │ with ctx: │
│ ❱ 788 │ │ │ │ return __callback(*ar │
│ 789 │ │
│ 790 │ def forward(__self, __cmd: "Comma │
│ 791 │ │ """Similar to :meth:`invoke` │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/cli.py:4126 in hyperpartition │
│ │
│ 4123 │ │ │ sys.exit(-1) │
│ 4124 │ │ │ hp.phased_merge_cluster(_ │
│ 4125 │ │ else: │
│ ❱ 4126 │ │ │ hp.incremental_partition( │
│ 4127 │ else: │
│ 4128 │ │ if merge_cluster: │
│ 4129 │ │ │ groups = list(_merge_clus │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/hyperpartition.py:1175 in │
│ incremental_partition │
│ │
│ 1172 │ │ │ # c = 5 * k[1] │
│ 1173 │ │ │ # else: │
│ 1174 │ │ │ # c = 60 │
│ ❱ 1175 │ │ │ self.alleletable = str(Pa │
│ 1176 │ │ │ │ │ │ │ │ │ │ │
│ 1177 │ │ │ │ │ │ │ │ │ │ │
│ 1178 │ │ │ │ │ │ │ │ │ │ │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/hyperpartition.py:920 in alleles │
│ │
│ 917 │ │ │ │ tl=25000, threads=4): │
│ 918 │ │ from .cli import alleles │
│ 919 │ │ try: │
│ ❱ 920 │ │ │ alleles.main( │
│ 921 │ │ │ │ args=[ │
│ 922 │ │ │ │ │ "-f", │
│ 923 │ │ │ │ │ str(fasta), │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/ri │
│ ch_click/rich_command.py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(c │
│ 127 │ │ │ │ │ if not standalone_ │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:1443 in invoke │
│ │
│ 1440 │ │ │ echo(style(message, fg="r │
│ 1441 │ │ │
│ 1442 │ │ if self.callback is not None: │
│ ❱ 1443 │ │ │ return ctx.invoke(self.ca │
│ 1444 │ │
│ 1445 │ def shell_complete(self, ctx: Con │
│ 1446 │ │ """Return a list of completio │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/cl │
│ ick/core.py:788 in invoke │
│ │
│ 785 │ │ │
│ 786 │ │ with augment_usage_errors(__s │
│ 787 │ │ │ with ctx: │
│ ❱ 788 │ │ │ │ return __callback(*ar │
│ 789 │ │
│ 790 │ def forward(__self, __cmd: "Comma │
│ 791 │ │ """Similar to :meth:`invoke` │
│ │
│ /public/home/lgl_xy/software/CPhasing/cphasi │
│ ng/cli.py:2671 in alleles │
│ │
│ 2668 │ │ logger.info("Identifing allel │
│ 2669 │ │ if len(args) > 0: │
│ 2670 │ │ │ with parallel_backend('lo │
│ ❱ 2671 │ │ │ │ Parallel(n_jobs=min(t │
│ args) │
│ 2672 │ │ │
│ 2673 │ │ else: │
│ 2674 │ │ │ logger.info("Load existin │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:2007 in __call__ │
│ │
│ 2004 │ │ # dispatch of the tasks to th │
│ 2005 │ │ next(output) │
│ 2006 │ │ │
│ ❱ 2007 │ │ return output if self.return_ │
│ 2008 │ │
│ 2009 │ def __repr__(self): │
│ 2010 │ │ return '%s(n_jobs=%s)' % (sel │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:1650 in _get_outputs │
│ │
│ 1647 │ │ │ yield │
│ 1648 │ │ │ │
│ 1649 │ │ │ with self._backend.retrie │
│ ❱ 1650 │ │ │ │ yield from self._retr │
│ 1651 │ │ │
│ 1652 │ │ except GeneratorExit: │
│ 1653 │ │ │ # The generator has been │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:1754 in _retrieve │
│ │
│ 1751 │ │ │ # exception (e.g. `Genera │
│ 1752 │ │ │ # worker traceback. │
│ 1753 │ │ │ if self._aborting: │
│ ❱ 1754 │ │ │ │ self._raise_error_fas │
│ 1755 │ │ │ │ break │
│ 1756 │ │ │ │
│ 1757 │ │ │ # If the next job is not │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:1789 in _raise_error_fast │
│ │
│ 1786 │ │ # calling get_result. This jo │
│ 1787 │ │ # called directly or if the g │
│ 1788 │ │ if error_job is not None: │
│ ❱ 1789 │ │ │ error_job.get_result(self │
│ 1790 │ │
│ 1791 │ def _warn_exit_early(self): │
│ 1792 │ │ """Warn the user if the gener │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:745 in get_result │
│ │
│ 742 │ │ │ # We assume that the resu │
│ 743 │ │ │ # callback thread, and is │
│ 744 │ │ │ # be returned. │
│ ❱ 745 │ │ │ return self._return_or_ra │
│ 746 │ │ │
│ 747 │ │ # For other backends, the mai │
│ 748 │ │ try: │
│ │
│ /public/home/lgl_xy/software/CPhasing/.pixi/ │
│ envs/default/lib/python3.12/site-packages/jo │
│ blib/parallel.py:763 in _return_or_raise │
│ │
│ 760 │ def _return_or_raise(self): │
│ 761 │ │ try: │
│ 762 │ │ │ if self.status == TASK_ER │
│ ❱ 763 │ │ │ │ raise self._result │
│ 764 │ │ │ return self._result │
│ 765 │ │ finally: │
│ 766 │ │ │ del self._result │
╰──────────────────────────────────────────────╯
ValueError: Duplicate key "Chr01g3"
现在又有一个新的问题了
你好，这个问题就是需要你们检查一下输入的fasta有没有重复的ID，还有就是你们输入的是用其它软件组装到染色体的fasta 吗？
谢谢，是的有重复ID，我们是根据组装效果，拆分成好几部分，使用了几个组装软件组装的结果。