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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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collapse trackback error #21

Open sidizhao opened 1 year ago

sidizhao commented 1 year ago

Hi, I've run ciri-long on 8 nanopore/pacbio samples and successfully completed this step. I'm unable to run the collapse command to completion:

ciri-long:v1.1.0 [Wed 2023-05-17 14:59:03] [INFO ] ----------------- Input paramters ------------------ [Wed 2023-05-17 14:59:03] [INFO ] Input reads: collapse.lst [Wed 2023-05-17 14:59:03] [INFO ] Output directory: collapse_output [Wed 2023-05-17 14:59:03] [INFO ] Multi threads: 16 [Wed 2023-05-17 14:59:03] [INFO ] -------------- Collapse circular reads ------------- [Wed 2023-05-17 14:59:03] [INFO ] Loading annotation gtf .. [Wed 2023-05-17 15:02:21] [INFO ] Loading additional circRNA bed .. [Wed 2023-05-17 15:02:21] [WARNING] Skipping 0 lines in bed file [Wed 2023-05-17 15:03:19] [INFO ] Step 1 - Clustering candidate circular reads [Wed 2023-05-17 15:03:49] [INFO ] Circular reads clusters: 103849 ^M[Wed 2023-05-17 15:45:45] [0% ] [..................................................]Trace back error: 4. Trace back error: 10. ^M[Wed 2023-05-17 16:29:10] [1% ] [..................................................]^M[Wed 2023-05-17 16:29:10] [2% ] [#.................................................]^M[Wed 2023-05-17 16:29:10] [3% ] [#.................................................]^M[Wed 2023-05-17 16:29:10] [4% ] [##................................................]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 "/usr/local/lib/python3.6/dist-packages/CIRI_long/collapse.py", line 227, in correct_chunk ret = correct_cluster(cluster, max_cluster=max_cluster) File "/usr/local/lib/python3.6/dist-packages/CIRI_long/collapse.py", line 265, in correct_cluster tmp = transform_seq(query.seq, alignment.query_begin) AttributeError: 'NoneType' object has no attribute 'query_begin' """

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

Traceback (most recent call last): File "/usr/local/bin/CIRI-long", line 8, in sys.exit(main()) File "/usr/local/lib/python3.6/dist-packages/CIRI_long/main.py", line 289, in main func(args) File "/usr/local/lib/python3.6/dist-packages/CIRI_long/main.py", line 196, in collapse circ_num, corrected_reads = collapse.correct_reads(reads_cluster, ref_fasta, gtf_idx, intron_idx, ss_idx, threads) File "/usr/local/lib/python3.6/dist-packages/CIRI_long/collapse.py", line 862, in correct_reads tmp_cluster, tmp_num = job.get() File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value AttributeError: 'NoneType' object has no attribute 'query_begin'