collapse trackback error

[sidizhao]

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'