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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
The text was updated successfully, but these errors were encountered:
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?
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:
--
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
Seon-Kyu Kim, Ph.D.
Principal Investigator
Aging Convergence Research Center
Personalized Genomic Medicine Research Center
Digital Biotech Innovation Center
@korea Research Institute of Bioscience and Biotechnology (KRIBB)
***@***.***
TEL: +82 42-879-8107
CP: +82 10-2840-7944
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
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:
Thank you for your assistance.
Best regards,
Seon-Kyu Kim
The text was updated successfully, but these errors were encountered: