search

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
6 stars 9 forks source link

error : Format Error! Z3 is not available! #11

Closed misik closed 5 years ago

misik commented 7 years ago

Hello,

After running the NCLScan for 24 hr I got this error. What can be the reason?

Thanks, Meltem

Read 63299 genes, 215674 transcripts and 1282859 exons from the gtf file.

novoindex (2.7) - Universal k-mer index constructor.

(C) 2008 - 2011 NovoCraft Technologies Sdn Bhd

novoindex MP1/MP1.JS2.ndx MP1/MP1.JS2.fa

Creating 12 indexing threads.

Building with 6-mer and step of 1 bp.

novoindex construction dT = 0.1s

Index memory size 0.000Gbyte.

Done.

Problem processing command line arguments: Expecting integer value for score threshold. at '-t' /opt/novocraft-2.07.18/novoalign -r A 1 -t 0,1 -d MP1/MP1.JS2.ndx -f MP1/MP1.main.unmapped_1.fastq MP1/MP1.main.unmapped_2.fastq --3Prime -o SAM Format Error! Z3 is not available! Format Error! Z3 is not available! Loaded 3227547748 letters in 524 sequences Searched 0 bases in 0 sequences Total time cost = 131.041696072 sec Loaded 198051268 letters in 94359 sequences Searched 0 bases in 0 sequences Total time cost = 12.3649411201 sec Loaded 28113910 letters in 27692 sequences Searched 0 bases in 0 sequences Total time cost = 2.79928803444 sec Loaded 33138 letters in 1 sequences Searched 0 bases in 0 sequences Total time cost = 2.7208340168 sec Format Error! Z3 is not available! Format Error! Z3 is not available! Traceback (most recent call last): File "NCLscan-1.6/bin/Add_read_count.py", line 118, in add_read_count(args.result_tmp_file, args.result_sam_file, args.output, args.JSParser_bin) File "NCLscan-1.6/bin/Add_read_count.py", line 13, in add_read_count all_junc_read_with_ref = get_junc_read(result_sam_data, JSParser_bin) File "NCLscan-1.6/bin/Add_read_count.py", line 66, in get_junc_read junc_read_data = get_read_with_ref(junc_read_sam_data) File "NCLscan-1.6/bin/Add_read_count.py", line 46, in get_read_with_ref ref_id = re.sub(".[0-9]*$", "", line[2]) IndexError: list index out of range Traceback (most recent call last): File "NCLscan-1.6/bin/get_gene_name.py", line 91, in add_gene_name(args.result_tmp_file, args.gene_anno, args.output) File "NCLscan-1.6/bin/get_gene_name.py", line 8, in add_gene_name result_tmp_data = read_TSV(result_tmp_file) File "NCLscan-1.6/bin/get_gene_name.py", line 64, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: 'MP1/MP1.result.tmp2' Traceback (most recent call last): File "NCLscan-1.6/NCLscan.py", line 448, in NCL_Scan4(config, datasets_list, args.project_name, args.output_dir) File "NCLscan-1.6/NCLscan.py", line 255, in NCL_Scan4 final_tmp = read_TSV("{prefix}.result.tmp3".format(**config_options)) File "NCLscan-1.6/NCLscan.py", line 279, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: 'MP1/MP1.result.tmp3'

chiangtw commented 5 years ago

NCLscan should be run with novoalign v3. It seems that the option "-t a,b" had not been available in novoalign v2.