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bioinfo-biols / CIRI-long

Circular RNA Identification for Nanopore Sequencing
https://ciri-cookbook.readthedocs.io
MIT License
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CIRI-long collapse showing error #3

Closed aman21392 closed 3 years ago

aman21392 commented 3 years ago

CIRI-long collapse -i ./test_call/test.lst -o /home/aclab/apps/CIRI-long/test_data/test_collapse/ -r mm10_chr12.fa -a mm10_chr12.gtf -t 70

[Mon 2021-03-15 15:46:07] [INFO ] ----------------- Input paramters ------------------ [Mon 2021-03-15 15:46:07] [INFO ] Input reads: test.lst [Mon 2021-03-15 15:46:07] [INFO ] Output directory: test_collapse [Mon 2021-03-15 15:46:07] [INFO ] Multi threads: 70 [Mon 2021-03-15 15:46:07] [INFO ] -------------- Collapse circular reads ------------- [Mon 2021-03-15 15:46:07] [INFO ] Loading pre-built splice site index from: /home/aclab/apps/CIRI-long/test_data/test_collapse/tmp/ss.idx [Mon 2021-03-15 15:46:08] [INFO ] Step 1 - Clustering candidate circular reads [Mon 2021-03-15 15:46:08] [INFO ] Circular reads clusters: 213 [Mon 2021-03-15 15:46:09] [0% ] [..................................................]multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/collapse.py", line 227, in correct_chunk ret = correct_cluster(cluster, max_cluster=max_cluster) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/collapse.py", line 406, in correct_cluster isoforms, circ_len = curate_isoform(circ, curated_exons, cluster_res) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/collapse.py", line 691, in curate_isoform tmp_isoform, tmp_len = merge_isoforms(circ, curated_exons, tmp_seq, tmp_ids) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/collapse.py", line 713, in merge_isoforms aligner = Aligner(seq, match=10, mismatch=4, gap_open=8, gap_extend=2) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/libs/striped_smith_waterman/ssw_wrap.py", line 134, in init self.set_ref(ref_seq) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/libs/striped_smith_waterman/ssw_wrap.py", line 167, in set_ref self.ref_seq = self._DNA_to_int_mat (ref_seq, self.ref_len) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/libs/striped_smith_waterman/ssw_wrap.py", line 245, in _DNA_to_int_mat value = self.base_to_int[seq[i]] TypeError: unhashable type: 'list' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/aclab/apps/pyspoa/pyspoa/bin/CIRI-long", line 33, in sys.exit(load_entry_point('CIRI-long==1.0', 'console_scripts', 'CIRI-long')()) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/main.py", line 246, in main args.func(args) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/main.py", line 160, in collapse circ_num, corrected_reads = collapse.correct_reads(reads_cluster, ref_fasta, gtf_idx, intron_idx, ss_idx, threads) File "/home/aclab/apps/pyspoa/pyspoa/lib/python3.6/site-packages/CIRI_long/collapse.py", line 861, in correct_reads tmp_cluster, tmp_num = job.get() File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value TypeError: unhashable type: 'list'

Can you please tell me why is it happen

Kevinzjy commented 3 years ago

Hi @aman21392, thanks for letting me aware. I've located a bug introduced when I switching from customized spoa cython API to pyspoa package and will upload a fixed version very soon.

Kevinzjy commented 3 years ago

Fixed in the latest version v1.0.1

aman21392 commented 3 years ago

So if I install directly from pip then it automatically installs the latest version or i have to download it from Github. Thanks

Kevinzjy commented 3 years ago

I've also updated CIRI-long on pypi.org, so pip install CIRI-long --upgrade should work fine.

aman21392 commented 3 years ago

OK thanks

aman21392 commented 3 years ago

Hi, I just want to know that after running CIRI-long test data how much circRNA we get. I got 157 circRNA, so is it the correct ones, when you run test data. Thanks in advance

Kevinzjy commented 3 years ago

Hi, I just want to know that after running CIRI-long test data how much circRNA we get. I got 157 circRNA, so is it the correct ones, when you run test data. Thanks in advance

Yes, it's the correct number in the test dataset.

aman21392 commented 3 years ago

Thanks a lot.

aman21392 commented 3 years ago

I just want to know you used a 30 nanopore dataset so how many circRNA found in each dataset. I want to know because I also run CIRI-long on those datasets. So can you please provide the circRNA no. in each dataset and how many are present in circAtlas in each datasets. Thanks in advance

Kevinzjy commented 3 years ago

You need to run the "collapse" command using all results from 32 libraries to get the final results, and use the expression matrix as final results. I haven't count the overlap of circAtlas in each dataset, but if you generated the matrix successfully, the results should be the same as that in our manuscript.

aman21392 commented 3 years ago

OK thanks, There is no human data only just mouse nanopore data. So all primers for validation in the paper have come from the mouse genome only.