"Aborted (core dumped)" during the align step in cassiopeia-preprocess

sk7944 commented 5 months ago

Hello,

I have set up the Cassiopeia tool and tested the data from SRR11357695 that you deposited in the GEO. During the align step in cassiopeia-preprocess, I encountered the error message "Aborted (core dumped)." It appears to be a memory deficiency issue on my machine. I would like to know the minimum system requirements to execute Cassiopeia.

Here are the specifications of the machine I used for testing Cassiopeia: OS: Ubuntu 22.04.4 LTS RAM: 128 GB

Here is the log of cassiopeia-preprocess from my machine:

(cancer_dormancy) sk7944@deepMUC:/data/cancer_dormancy/GSE146712.lineage_tracing$ cassiopeia-preprocess preprocess.SRR11357695.cfg 
[2024-05-28 14:42:56,719]    INFO [main] Starting...
[2024-05-28 14:42:56,721]   DEBUG [collapse] Keyword arguments: {'max_hq_mismatches': 3, 'max_indels': 2, 'method': 'cutoff', 'output_directory': '/data/cancer_dormancy/GSE146712.lineage_tracing/output', 'n_threads': 32}
[2024-05-28 14:42:56,721]    INFO [collapse] Starting...
[2024-05-28 14:42:56,721]    INFO [collapse] Using BAM tag `CB` as cell barcodes
Merging sorted chunks: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 23331100/23331100 [01:31<00:00, 255087.90it/s]
[2024-05-28 14:48:41,220]    INFO [collapse] Sorted bam directory saved to /data/cancer_dormancy/GSE146712.lineage_tracing/output/SRR11357695_unmapped_filtered_corrected_sorted.bam
[2024-05-28 14:48:41,221]    INFO [collapse] Max read length of 285
[2024-05-28 14:48:41,221]    INFO [collapse] Total reads: 23331100
Collapsing UMIs: 100%|##############################################################################################################################################################################| 900668/900668 [03:06<00:00, 4837.84it/s]
Writing collapsed UMIs: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 900668/900668 [00:06<00:00, 139838.20it/s]
[2024-05-28 14:54:05,433]    INFO [collapse] Collapsed bam directory saved to /data/cancer_dormancy/GSE146712.lineage_tracing/output/SRR11357695_unmapped_filtered_corrected_sorted.collapsed.bam
[2024-05-28 14:54:05,434]    INFO [collapse] Converted dataframe saved to /data/cancer_dormancy/GSE146712.lineage_tracing/output/SRR11357695_unmapped_filtered_corrected_sorted.collapsed.txt
[2024-05-28 14:54:05,434]    INFO [collapse] Finished in 668.7130060195923 s.
[2024-05-28 14:54:42,796]   DEBUG [resolve] Keyword arguments: {'min_avg_reads_per_umi': 2.0, 'min_umi_per_cell': 10, 'plot': True, 'output_directory': '/data/cancer_dormancy/GSE146712.lineage_tracing/output'}
[2024-05-28 14:54:42,796]    INFO [resolve] Starting...
Resolving UMI sequences: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 900668/900668 [01:40<00:00, 8956.33it/s]
[2024-05-28 14:56:29,431]    INFO [resolve] Filtered out 1470392 reads.
[2024-05-28 14:56:32,090]    INFO [resolve] Filtered out 112438 cells with too few UMIs or too few average number of reads per UMI.
[2024-05-28 14:56:32,154]    INFO [resolve] Filtered out 487383 UMIs as a result.
[2024-05-28 14:56:32,363]   DEBUG [resolve] Resulting molecule_table statistics:
[2024-05-28 14:56:32,364]   DEBUG [resolve] # Reads: 20219281
[2024-05-28 14:56:32,364]   DEBUG [resolve] # UMIs: 413285
[2024-05-28 14:56:32,422]   DEBUG [resolve] # Cell BCs: 2594
[2024-05-28 14:56:32,897]    INFO [resolve] Finished in 110.1008095741272 s.
[2024-05-28 14:56:39,348]   DEBUG [align] Keyword arguments: {'gap_open_penalty': 20, 'gap_extend_penalty': 1, 'method': 'local', 'ref_filepath': '/data/cancer_dormancy/GSE146712.lineage_tracing/data/PCT48.ref.fasta', 'ref': None, 'n_threads': 32}
[2024-05-28 14:56:39,349]    INFO [align] Starting...
Aligning sequences to reference:   9%|##############7                                                                                                                                                 | 17732/192928 [00:23<03:55, 743.04it/s]Exception ignored in: <function Image.__del__ at 0x73411a746ee0>
Traceback (most recent call last):
  File "/home/sk7944/anaconda3/envs/cancer_dormancy/lib/python3.9/tkinter/__init__.py", line 4017, in __del__
    self.tk.call('image', 'delete', self.name)
RuntimeError: main thread is not in main loop
Exception ignored in: <function Variable.__del__ at 0x73411a72f5e0>
Traceback (most recent call last):
  File "/home/sk7944/anaconda3/envs/cancer_dormancy/lib/python3.9/tkinter/__init__.py", line 363, in __del__
    if self._tk.getboolean(self._tk.call("info", "exists", self._name)):
RuntimeError: main thread is not in main loop
Exception ignored in: <function Variable.__del__ at 0x73411a72f5e0>
Traceback (most recent call last):
  File "/home/sk7944/anaconda3/envs/cancer_dormancy/lib/python3.9/tkinter/__init__.py", line 363, in __del__
    if self._tk.getboolean(self._tk.call("info", "exists", self._name)):
RuntimeError: main thread is not in main loop
Exception ignored in: <function Variable.__del__ at 0x73411a72f5e0>
Traceback (most recent call last):
  File "/home/sk7944/anaconda3/envs/cancer_dormancy/lib/python3.9/tkinter/__init__.py", line 363, in __del__
    if self._tk.getboolean(self._tk.call("info", "exists", self._name)):
RuntimeError: main thread is not in main loop
Exception ignored in: <function Variable.__del__ at 0x73411a72f5e0>
Traceback (most recent call last):
  File "/home/sk7944/anaconda3/envs/cancer_dormancy/lib/python3.9/tkinter/__init__.py", line 363, in __del__
    if self._tk.getboolean(self._tk.call("info", "exists", self._name)):
RuntimeError: main thread is not in main loop
Tcl_AsyncDelete: async handler deleted by the wrong thread
**Aborted (core dumped)**

Thank you for your assistance.

Best regards, Seon-Kyu Kim

colganwi commented 3 months ago

128 GB should be more than enough RAM. I can't figure out what the problem is from the traceback. Cassiopeia does not call tkinter directly. Have you been able to resolve the issue?

sk7944 commented 3 months ago

After upgrading the memory to more than 128GB, the error disappeared. Thank you for your advice.

2024년 7월 13일 (토) 오전 7:42, William Colgan @.***>님이 작성:

128 GB should be more than enough RAM. I can't figure out what the problem is from the traceback. Cassiopeia does not call tkinter directly. Have you been able to resolve the issue?

— Reply to this email directly, view it on GitHub https://github.com/YosefLab/Cassiopeia/issues/243#issuecomment-2226449671, or unsubscribe https://github.com/notifications/unsubscribe-auth/AU7KN6DQ3NNYTVKDVJ3REEDZMBLVDAVCNFSM6AAAAABIMN2STSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRWGQ2DSNRXGE . You are receiving this because you authored the thread.Message ID: @.***>

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YosefLab / Cassiopeia

"Aborted (core dumped)" during the align step in cassiopeia-preprocess #243