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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
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FileNotFoundError: Did not find file SMA/outs/filtered/matrix.mtx.gz. #289

Open 2124sa opened 3 weeks ago

2124sa commented 3 weeks ago

Hello, I encountered this error while running CeleScope. Exiting because of FATAL ERROR: could not create FIFO file .//SMA/01.starsolo/SMA__STARtmp/tmp.fifo.read1 SOLUTION: check the if run directory supports FIFO files. If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), re-run on a Linux partition, or point --outTmpDir to a Linux partition.

Jun 13 19:29:03 ...... FATAL ERROR, exiting Traceback (most recent call last): File "/home/a2433/miniconda3/envs/celescope/bin/celescope", line 8, in sys.exit(main()) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main args.func(args) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 186, in starsolo q30_cb, q30_umi, chemistry = runner.run() File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 177, in run self.run_starsolo() File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 133, in run_starsolo subprocess.check_call(cmd, shell=True) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'STAR \ --genomeDir /mnt/e/sting/test_dir/Mm \ --readFilesIn /mnt/e/STING/scrnaseq/CleanData/SMA/SMA_2.fastq.gz /mnt/e/STING/scrnaseq/CleanData/SMA/SMA_1.fastq.gz \ --readFilesCommand zcat \ --soloCBwhitelist None \ --soloCellFilter EmptyDropsCR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 \ --outFileNamePrefix .//SMA/01.starsolo/SMA \ --runThreadN 4 \ --clip3pAdapterSeq AAAAAAAAAAAA \ --outFilterMatchNmin 50 \ --soloFeatures Gene GeneFull_Ex50pAS \ --outSAMattributes NH HI nM AS CR UR CB UB GX GN \ --soloType CB_UMI_Simple \ --soloCBstart 1 --soloCBlen 12 \ --soloUMIstart 13 --soloUMIlen 8 \ --soloCBmatchWLtype 1MM \ --outSAMtype BAM SortedByCoordinate \ --soloCellReadStats Standard \ --soloBarcodeReadLength 0 \ ' returned non-zero exit status 112. 2024-06-13 19:29:04,273 - celescope.rna.analysis.analysis - INFO - start... CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/mnt/e/sting/test_dir/Mm', matrix_file='.//SMA/outs/filtered', outdir='.//SMA/02.analysis', sample='SMA', thread='4', debug=False, func=<function analysis at 0x7fbee36d5550>) CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/mnt/e/sting/test_dir/Mm', matrix_file='.//SMA/outs/filtered', outdir='.//SMA/02.analysis', sample='SMA', thread='4', debug=False, func=<function analysis at 0x7fbee36d5550>) Traceback (most recent call last): File "/home/a2433/miniconda3/envs/celescope/bin/celescope", line 8, in sys.exit(main()) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main args.func(args) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper result = func(*args, **kwargs) File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis runner.run() File "/home/a2433/miniconda3/envs/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 "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in init self.adata = sc.read_10x_mtx( File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx adata = read( File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx adata = read( File "/home/a2433/miniconda3/envs/celescope/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read return _read( File "/home/a2433/miniconda3/envs/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 SMA/outs/filtered/matrix.mtx.gz.

I employed two methodologies, both of which proved futile.

  1. nohup sh ./shell/*.sh &
  2. sh /mnt/e/sting/scrnaseq/CleanData/shell/SMA.sh

I obtained shell access through this command. multi_rna --mapfile ./my.mapfile.txt --genomeDir /mnt/e/sting/test_dir/Mm --thread 4 --mod shell --chemistry scopeV1

Here is my mapfile document. SMA /mnt/e/STING/scrnaseq/CleanData/SMA SMA SMC /mnt/e/STING/scrnaseq/CleanData/SMC SMC

I eagerly anticipate your assistance！

zhouyiqi91 commented 3 weeks ago 
Exiting because of FATAL ERROR: could not create FIFO file .//SMA/01.starsolo/SMA__STARtmp/tmp.fifo.read1
SOLUTION: check the if run directory supports FIFO files.
If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), re-run on a Linux partition, or point --outTmpDir to a Linux partition.

You can re-run on a Linux partition, or point --outTmpDir to a Linux partition by adding --STAR_param "--outTmpDir some_linux_dir" to multi_rna