(celescope)dbax@cn45:/scratch/dbax/dynascope/singleron_script$ "/scratch/dbax/dynascope/singleron_script/run.sh"
2024-03-04 18:25:22,873 - celescope.tools.multi.parse_mapfile - INFO - start...
2024-03-04 18:25:22,875 - celescope.tools.multi.parse_mapfile - INFO - done. time used: 0:00:00.002605
(celescope)dbax@cn45:/scratch/dbax/dynascope/singleron_script$ "/scratch/dbax/dynascope/singleron_script/shell/4sU_72h.sh"
-bash: /scratch/dbax/dynascope/singleron_script/shell/4sU_72h.sh: Permission denied
(celescope)dbax@cn45:/scratch/dbax/dynascope/singleron_script$ chmod +x "/scratch/dbax/dynascope/singleron_script/shell/4sU_72h.sh"
(celescope)dbax@cn45:/scratch/dbax/dynascope/singleron_script$ "/scratch/dbax/dynascope/singleron_script/shell/4sU_72h.sh"
2024-03-04 18:26:38,433 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', outdir='.//4sU_72h/00.sample', sample='4sU_72h', thread='8', debug=False, fq1='/scratch/dbax/dynascope/singleron_72/4SU_S2_L001_R1_001.fastq.gz', chemistry='auto', wells=384, func=<function sample at 0x149e9b101550>)
2024-03-04 18:26:38,438 - celescope.tools.sample.run - INFO - start...
2024-03-04 18:26:38,687 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-03-04 18:26:38,687 - celescope.tools.barcode.check_chemistry - INFO - /scratch/dbax/dynascope/singleron_72/4SU_S2_L001_R1_001.fastq.gz
2024-03-04 18:26:38,687 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/sample.py", line 68, in sample
    runner.run()
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/sample.py", line 36, in run
    chemistry = ch.check_chemistry()
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
    chemistry = self.get_chemistry(fastq1)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
    chemistry = self.seq_chemistry(seq)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
    linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
    raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: GNGGATTGACGTTGATGTTGGTCTCTGAGTAGTCGACTTCGTATTAGCTTTGTAGGGCT
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', chemistry='auto', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/scratch/dbax/dynascope/mmu_ensembl_99/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='--outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3', SAM_attributes='MD', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/scratch/dbax/dynascope/singleron_72/4SU_S2_L001_R1_001.fastq.gz', fq2='/scratch/dbax/dynascope/singleron_72/4SU_S2_L001_R2_001.fastq.gz', outdir='.//4sU_72h/01.starsolo', sample='4sU_72h', thread='8', debug=False, func=<function starsolo at 0x147800742dc0>)
2024-03-04 18:26:40,849 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-03-04 18:26:40,849 - celescope.tools.barcode.check_chemistry - INFO - /scratch/dbax/dynascope/singleron_72/4SU_S2_L001_R1_001.fastq.gz
2024-03-04 18:26:40,849 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 185, in starsolo
    with Starsolo(args) as runner:
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 41, in __init__
    chemistry_list = ch.check_chemistry()
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
    chemistry = self.get_chemistry(fastq1)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
    chemistry = self.seq_chemistry(seq)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
    linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
    raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: GNGGATTGACGTTGATGTTGGTCTCTGAGTAGTCGACTTCGTATTAGCTTTGTAGGGCT
2024-03-04 18:26:42,950 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', genomeDir='/scratch/dbax/dynascope/mmu_ensembl_99/', matrix_file='.//4sU_72h/outs/filtered', outdir='.//4sU_72h/02.analysis', sample='4sU_72h', thread='8', debug=False, func=<function analysis at 0x14ab512eaee0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', genomeDir='/scratch/dbax/dynascope/mmu_ensembl_99/', matrix_file='.//4sU_72h/outs/filtered', outdir='.//4sU_72h/02.analysis', sample='4sU_72h', thread='8', debug=False, func=<function analysis at 0x14ab512eaee0>)
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
    runner.run()
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
    with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in __init__
    self.adata = sc.read_10x_mtx(
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
    adata = read(
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
    adata = read(
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
    return _read(
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
    raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file 4sU_72h/outs/filtered/matrix.mtx.gz.
2024-03-04 18:26:44,900 - celescope.dynaseq.conversion.conversion - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', genomeDir='/scratch/dbax/dynascope/mmu_ensembl_99/', basequalilty=20, snp_min_cells=10.0, snp_min_depth=20, cellsplit=300, conversionMem=30, bam='.//4sU_72h/outs/4sU_72h_Aligned.sortedByCoord.out.bam', cell='.//4sU_72h/outs/filtered/barcodes.tsv.gz', outdir='.//4sU_72h/03.conversion', sample='4sU_72h', thread='8', debug=False, func=<function conversion at 0x146b7150e820>)
2024-03-04 18:26:44,903 - celescope.tools.reference.get_id_name - INFO - start...
2024-03-04 18:28:11,902 - celescope.tools.reference.get_id_name - INFO - done. time used: 0:01:26.998303
2024-03-04 18:28:11,903 - celescope.tools.utils.barcode_list_stamp - INFO - start...
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/conversion.py", line 287, in conversion
    with Conversion(args) as runner:
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/conversion.py", line 46, in __init__
    self.cell_dict, self.cell_num = utils.barcode_list_stamp(self.bcfile,cut=self.cellsplit)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 599, in barcode_list_stamp
    bc_list, bc_num = read_one_col(barcode_list)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 142, in read_one_col
    df = pd.read_csv(file, header=None)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 933, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine
    self.handles = get_handle(  # type: ignore[call-overload]
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/common.py", line 714, in get_handle
    handle = gzip.GzipFile(  # type: ignore[assignment]
  File "/vol/mbconda/dbax/celescope/lib/python3.9/gzip.py", line 173, in __init__
    fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: './/4sU_72h/outs/filtered/barcodes.tsv.gz'
2024-03-04 18:28:14,391 - celescope.dynaseq.substitution.substitution - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', bam='.//4sU_72h/03.conversion/4sU_72h.PosTag.bam', outdir='.//4sU_72h/04.substitution', sample='4sU_72h', thread='8', debug=False, func=<function substitution at 0x1510d8156310>)
2024-03-04 18:28:14,394 - celescope.dynaseq.substitution.run - INFO - start...
2024-03-04 18:28:14,394 - celescope.dynaseq.substitution.get_sub_tag - INFO - start...
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/substitution.py", line 123, in substitution
    runner.run()
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/substitution.py", line 37, in run
    for_base, rev_base, is_forward, is_reverse = self.get_sub_tag(self.bam_file)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/substitution.py", line 46, in get_sub_tag
    bamfile = pysam.AlignmentFile(bam, 'rb', require_index=False)
  File "pysam/libcalignmentfile.pyx", line 748, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `.//4sU_72h/03.conversion/4sU_72h.PosTag.bam`: No such file or directory
2024-03-04 18:28:16,300 - celescope.dynaseq.replacement.replacement - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='dynaseq', genomeDir='/scratch/dbax/dynascope/mmu_ensembl_99/', control=False, cellsplit=300, bam='.//4sU_72h/03.conversion/4sU_72h.PosTag.bam', cell='.//4sU_72h/outs/filtered/barcodes.tsv.gz', bg=['.//4sU_72h/03.conversion/4sU_72h.snp.csv'], tsne='.//4sU_72h/outs/tsne_coord.tsv', outdir='.//4sU_72h/05.replacement', sample='4sU_72h', thread='8', debug=False, func=<function replacement at 0x1529d8be24c0>)
2024-03-04 18:28:16,303 - celescope.tools.utils.barcode_list_stamp - INFO - start...
Traceback (most recent call last):
  File "/vol/mbconda/dbax/celescope/bin/celescope", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
    args.func(args)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/replacement.py", line 300, in replacement
    with Replacement(args, display_title='Labeled') as runner:
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/dynaseq/replacement.py", line 53, in __init__
    self.cell_dict, self.cell_num = utils.barcode_list_stamp(self.bcfile,cut=self.cellsplit)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
    result = func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 599, in barcode_list_stamp
    bc_list, bc_num = read_one_col(barcode_list)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 142, in read_one_col
    df = pd.read_csv(file, header=None)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 933, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine
    self.handles = get_handle(  # type: ignore[call-overload]
  File "/vol/mbconda/dbax/celescope/lib/python3.9/site-packages/pandas/io/common.py", line 714, in get_handle
    handle = gzip.GzipFile(  # type: ignore[assignment]
  File "/vol/mbconda/dbax/celescope/lib/python3.9/gzip.py", line 173, in __init__
    fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: './/4sU_72h/outs/filtered/barcodes.tsv.gz'