(base) lenovo@lenovo-ThinkStation-P2-Tower:/media/lenovo/E676335D76332E25/SCLC_rna-seq$ docker run -v $PWD:/media/lenovo/E676335D76332E25/SCLC_rna-seq -t frankligy123/altanalyze:0.7.0.1 identify bam 107
Current folder is /mnt
Identify splicing junction, bam folder is /mnt/bam, using 107 cores
/usr/src/app/AltAnalyze.sh: line 114: cd: /mnt/bam: No such file or directory
start to get junction bed
library lxml not supported. WikiPathways and LineageProfiler visualization will not work. Please install with pip install lxml.
start to get exon bed
[E::hts_open_format] Failed to open file /mnt/bam/*.bam
Traceback (most recent call last):
File "/usr/src/app/altanalyze/import_scripts/BAMtoJunctionBED.py", line 355, in <module>
try: parseJunctionEntries(bam_dir,Species=Species,ReferenceDir=reference_dir)
File "/usr/src/app/altanalyze/import_scripts/BAMtoJunctionBED.py", line 232, in parseJunctionEntries
bamf = pysam.Samfile(bam_dir, "rb" , check_sq=False)
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file `/mnt/bam/*.bam`: No such file or directory
[E::hts_open_format] Failed to open file /mnt/bam/*.bam
Traceback (most recent call last):
File "/usr/src/app/altanalyze/import_scripts/BAMtoExonBED.py", line 417, in <module>
parseExonReferences(bam_dir,reference_dir,intronRetentionOnly=True,species=species)
File "/usr/src/app/altanalyze/import_scripts/BAMtoExonBED.py", line 70, in parseExonReferences
bamfile = pysam.Samfile(bam_dir, "rb" )
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file `/mnt/bam/*.bam`: No such file or directory
/usr/src/app/AltAnalyze.sh: line 126: cd: /mnt/bam: No such file or directory
mv: cannot stat '*.bed': No such file or directory
library lxml not supported. WikiPathways and LineageProfiler visualization will not work. Please install with pip install lxml.
Starting AltAnalyze version 2.1.4.4
Using the Config location: /usr/src/app/altanalyze/Config//report.log
/usr/src/app/altanalyze/Config//options.txt
Options.txt found in local Config = True ...confirmed found
AltAnalyze depedency not met for: patsy
...Combat batch effects correction requires pandas and patsy
AltAnalyze depedency not met for: wx
...The AltAnalyze Results Viewer requires wx
AltAnalyze depedency not met for: fastcluster
...Faster hierarchical cluster not supported without fastcluster
AltAnalyze depedency not met for: lxml
...Wikipathways visualization not supported without lxml
WARNING!!!! Some dependencies are not currently met.
This may impact AltAnalyze's performance
Running commandline options
Arguments input: ['/usr/src/app/altanalyze/AltAnalyze.py', '--species', 'Hs', '--platform', 'RNASeq', '--version', 'EnsMart91', '--bedDir', '/mnt/bed', '--output', '/mnt/altanalyze_output', '--groupdir', '/mnt/altanalyze_output/ExpressionInput/groups.original.txt', '--compdir', '/mnt/altanalyze_output/ExpressionInput/comps.original.txt', '--expname', 'original', '--runGOElite', 'no']
Current database version: EnsMart91
Traceback (most recent call last):
File "/usr/src/app/altanalyze/AltAnalyze.py", line 7819, in commandLineRun
log_report = open(log_file,'w'); log_report.close()
IOError: [Errno 2] No such file or directory: '/mnt/altanalyze_output/AltAnalyze_report-20250826-125843.log'
Please designate an output directory before proceeding (e.g., --output "C:\RNASeq)
prune the raw junction count matrix
Traceback (most recent call last):
File "/usr/src/app/prune.py", line 8, in <module>
df = pd.read_csv('/mnt/altanalyze_output/ExpressionInput/counts.original.txt',sep='\t',index_col=0)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 678, in parser_f
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 440, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 787, in __init__
self._make_engine(self.engine)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 1014, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 1708, in __init__
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 384, in pandas._libs.parsers.TextReader.__cinit__
File "pandas/_libs/parsers.pyx", line 695, in pandas._libs.parsers.TextReader._setup_parser_source
IOError: File /mnt/altanalyze_output/ExpressionInput/counts.original.txt does not exist
本文解决了在使用Visual Studio搭建wxWidgets开发环境时遇到的“无法打开包括文件:‘wx/setup.h’”的问题。解决方案是从安装目录的lib路径下找到相关文件并复制到include目录。
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