Xenocell - Error in classify reads
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6 months ago
c2e09af0 • 0

Hello everyone, I'm trying to run Xenocell on my dataset. I have some problems executing the "classify reads" step. The command terminates after starting the classification ("terminate called after throwing an instance of 'std::ios_base::failure'"). and I don't know how to fix the error. Any help would be appreciated. Thank you!

(base) -bash-4.2$ singularity exec xenocell_1.0.sif xenocell.py classify_reads --transcript /scratch/path/fastq/S2_L001_R2_001.fastq.gz --barcode /scratch/path/fastq/S2_L001_R1_001.fastq.gz  --barcode_start 1 --barcode_length 16 --index /scratch/path/xenocell/xenome --output /scratch/path/xenocell/S2 --threads 16 --memory 70 --compression_level 1
## XenoCell: Classify reads and generate table of cellular barcodes.
## FASTQ file containing transcript:       /scratch/path/fastq/S2_L001_R2_001.fastq.gz
## FASTQ file containing cellular barcode: /scratch/path/fastq/S2_L001_R1_001.fastq.gz
## Barcode starting position:              1
## Length of cellular barcode:             16
## Path to Xenome index:                   /scratch/path/xenocell/xenome
## Output directory:                       /scratch/path/xenocell/S2
## Keep Xenome output files:               False
## Number of threads:                      16
## Memory in GB:                           70
## Compression level:                      1
[2023-03-15 08:48:52] De-compress FASTQ files before classifying...
[2023-03-15 09:10:32] Start classification...
terminate called after throwing an instance of 'std::ios_base::failure'
  what():  basic_ios::clear
[2023-03-15 09:51:43] Fix FASTQ format...
sed: couldn't write 67 items to stdout: Disk quota exceeded
sed: couldn't write 150 items to stdout: Broken pipe
sed: couldn't write 66 items to stdout: Disk quota exceeded
sed: couldn't write 150 items to stdout: Broken pipe
[2023-03-15 09:51:43] Create list of read names to extract...
[2023-03-15 09:51:43] Extract reads...
[2023-03-15 09:58:03] Generate table of cellular barcodes and associated read counts...
Traceback (most recent call last):
  File "/XenoCell/python/xenocell.py", line 297, in <module>
  File "/XenoCell/python/xenocell.py", line 35, in main
  File "/XenoCell/python/classify_reads.py", line 96, in classify_reads
    df_barcodes_all = generate_barcode_table('fq_barcode_graft.fq', 'fq_barcode_host.fq', barcode_start_position, barcode_end_position)
  File "/XenoCell/python/classify_reads.py", line 240, in generate_barcode_table
    barcodes_graft.columns = ['barcode', 'graft']
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/generic.py", line 5478, in __setattr__
    return object.__setattr__(self, name, value)
  File "pandas/_libs/properties.pyx", line 66, in pandas._libs.properties.AxisProperty.__set__
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/generic.py", line 670, in _set_axis
    self._mgr.set_axis(axis, labels)
  File "/opt/conda/lib/python3.7/site-packages/pandas/core/internals/managers.py", line 221, in set_axis
    f"Length mismatch: Expected axis has {old_len} elements, new "
ValueError: Length mismatch: Expected axis has 1 elements, new values have 2 elements
Xenocell PDX scRNAseq singularity-container • 350 views
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Disk quota exceeded


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I wasn't sure if this is the initial problem since this message turns up later than the first error message


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