Closed aman21392 closed 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.
Fixed in the latest version v1.0.1
So if I install directly from pip then it automatically installs the latest version or i have to download it from Github. Thanks
I've also updated CIRI-long on pypi.org, so pip install CIRI-long --upgrade
should work fine.
OK thanks
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
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.
Thanks a lot.
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
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.
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.
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