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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can not generate the CircRNA with NCLscan version #29

Open JianGuoZhou3 opened 1 year ago

JianGuoZhou3 commented 1 year ago
(base) zhou2@zhou2-Super-Server:~$ conda activate kn

(kn) zhou2@zhou2-Super-Server:~$ 
(kn) zhou2@zhou2-Super-Server:~$ /home/zhou2/soft/NCLscan-1.7.0/NCLscan.py
usage: NCLscan.py [-h] [-c CONFIG] [--fq1 FQ1] [--fq2 FQ2] [-pj PROJECT_NAME]
                  [-o OUTPUT_DIR]

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        The config file of NCLscan.
  --fq1 FQ1             The 1st end of the paired-end reads.
  --fq2 FQ2             The 2nd end of the paired-end reads.
  -pj PROJECT_NAME, --project_name PROJECT_NAME
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
(kn) zhou2@zhou2-Super-Server:~$ 
JianGuoZhou3 commented 1 year ago
    nohup /home/zhou2/soft/NCLscan-1.7.0/NCLscan.py -c /home/zhou2/soft/NCLscan-1.7.0/NCLscan.config -pj raw -o ${dir}/NCLscan/${i}.output --fq1 ${dir}/raw/${i}_1.fastq.gz --fq2 ${dir}/raw/${i}_2.fastq.gz

There are some errors.

# novoindex (4.3) - Universal k-mer index constructor.
# (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd
# novoindex /home/data/EGA/IMmotion151/NCLscan/WO29637_ngs_rna_targrna_EA_001b0af504.output/raw.JS2.ndx /home/data/EGA/IMmotion151/NCLscan/WO29637_ngs_rna_targrna_EA_001b0af504.output/raw.JS2.fa 
# Creating 127 indexing threads.
# Building with 9-mer and step of 1 bp.
#             0 kmers were indexed.
#             0 kmers not indexed due to excess N's.
# novoindex construction dT = 0.0s
# Index memory size   0.001Gbyte.
# Done.
Error: /home/data/EGA/IMmotion151/NCLscan/WO29637_ngs_rna_targrna_EA_001b0af504.output/raw.JS2.ndx does not appear to be a valid novoindex. Code 9
Start to split the input into 20 part ... 
Traceback (most recent call last):
  File "/home/zhou2/soft/NCLscan-1.7.0/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/zhou2/soft/NCLscan-1.7.0/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
JianGuoZhou3 commented 1 year ago

nohup.out.txt

JianGuoZhou3 commented 1 year ago

@TreesLab @chiangtw @chenchiaying