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TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
MIT License
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NCLscan CAN NOT work anymore, it belongs to the License that expired on 9 Aug 2021? #27

Closed JianGuoZhou3 closed 2 years ago

JianGuoZhou3 commented 2 years ago 
# Creating 95 indexing threads.
# License file: /home/zhou/miniconda2/envs/kn/bin/novoalign.lic
# License expired on 9 Aug 2021.
# System Local time: Sun Jan 23 15:05:20 2022
Problem processing command line arguments: Licensing: --3Prime option is not available in unlicensed versions. at arg[11 of 14] '--3Prime'
Novoalign*: For full list of options enter /home/zhou/miniconda2/envs/kn/bin/novoalign --help
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 152, in <module>
    mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt)
  File "/home/zhou/soft/NCLscan/bin/mp_blat.py", line 72, in mp_blat
    edge_pos = [all_reads_pos[0]] + splice_positions + [fasta_file_size]
IndexError: list index out of range
cat: /home/zhou/raid/TCGA_BLCA/RNA_seq/NCLscan/TCGA_BT_A20U_01A.output/raw.rG.um3.psl: 没有那个文件或目录
cat: /home/zhou/raid/TCGA_BLCA/RNA_seq/NCLscan/TCGA_BT_A20U_01A.output/raw.coding.um3.psl: 没有那个文件或目录
cat: /home/zhou/raid/TCGA_BLCA/RNA_seq/NCLscan/TCGA_BT_A20U_01A.output/raw.lncRNA.um3.psl: 没有那个文件或目录
cat: /home/zhou/raid/TCGA_BLCA/RNA_seq/NCLscan/TCGA_BT_A20U_01A.output/raw.chrM.um3.psl: 没有那个文件或目录

Dear @TreesLab @chiangtw NCLscan CAN NOT work anymore, it belongs to the License that expired on 9 Aug 2021? Best,. Jian-Guo