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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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why look for tools in the current working directory? #3

Closed brianjohnhaas closed 8 years ago

brianjohnhaas commented 8 years ago

Is it possible to have the software just look for tools either in the installation directory or via the PATH setting?

./NCLscan.sh simu_5X_100PE_1.fastq simu_5X_100PE_2.fastq 0 8 50 ========== Start ===========

Mon Feb 29 13:23:48 EST 2016

sh: ./bwa: No such file or directory [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! Traceback (most recent call last): File "./NCL_Scan0.py", line 43, in main() File "./NCL_Scan0.py", line 38, in main get_bwa_unmapped(args.Fastq_1, args.Fastq_2, args.Project_Name, args.bwa_index_prefix, args.bwa_thread) File "./NCL_Scan0.py", line 12, in get_bwa_unmapped os.mkdir("split_unmap.tmp") OSError: [Errno 17] File exists: 'split_unmap.tmp' cat: GRCh37.p13.genome.fa: No such file or directory cat: GRCh37.p13.genome.fa: No such file or directory cat: gencode.v19.pc_transcripts.fa: No such file or directory cat: gencode.v19.lncRNA_transcripts.fa: No such file or directory sh: ./novoindex: No such file or directory sh: ./novoalign: No such file or directory cat: 0.bwa.unmapped_1.fastq: No such file or directory cat: 0.bwa.unmapped_2.fastq: No such file or directory sh: ./blat: No such file or directory cat: 0.rG.psl: No such file or directory cat: 0.rG.psl: No such file or directory PslChimeraFilter v0.4

sh: ./blat: No such file or directory sh: ./blat: No such file or directory sh: ./blat: No such file or directory cat: 0.coding.2.psl: No such file or directory cat: 0.lncRNA.2.psl: No such file or directory cat: 0.chrM.2.psl: No such file or directory JunctionSite2BED v0.3

Get annotation of exonic regions beginnig from exons colsed to a given position.

Example: cat Pos.bed | ./JunctionSite2BED gencode.v18.annotation.gtf 500 300

Format Error! Format Error! sh: ./bedtools: No such file or directory cat: 0.preJS.seq: No such file or directory Format Error! Format Error! NCL_Scan3 v0.5 ./NCL_Scan3 (null) sh: ./novoindex: No such file or directory sh: ./novoalign: No such file or directory sh: ./novoalign: No such file or directory sh: ./blat: No such file or directory cat: 0.JS.GRCh37.psl: No such file or directory sh: ./blat: No such file or directory cat: 0.2.info.GRCh37.psl: No such file or directory PslChimeraFilter v0.4

JunctionSite2BED v0.3

Get annotation of exonic regions beginnig from exons colsed to a given position.

Example: cat Pos.bed | ./JunctionSite2BED gencode.v18.annotation.gtf 500 300

Format Error! Format Error! sh: ./bedtools: No such file or directory cat: 0.PreJS2.seq: No such file or directory Format Error! Format Error! sh: ./novoindex: No such file or directory NCLScan4 v0.2.5 sh: ./novoalign: No such file or directory rm: cannot remove '.um3.psl': No such file or directory sh: ./blat: No such file or directory sh: ./blat: No such file or directory sh: ./blat: No such file or directory sh: ./blat: No such file or directory cat: *.um3.psl: No such file or directory Traceback (most recent call last): File "./Add_read_count.py", line 92, in main() File "./Add_read_count.py", line 88, in main add_read_count(res_tmp_file, res_sam_file, output_file, args.JSParser_bin) File "./Add_read_count.py", line 13, in add_read_count all_junc_read_with_ref = get_junc_read(result_sam_data, JSParser_bin) File "./Add_read_count.py", line 66, in get_junc_read junc_read_data = get_read_with_ref(junc_read_sam_data) File "./Add_read_count.py", line 46, in get_read_with_ref refid = re.sub(".[0-9]$", "", line[2]) IndexError: list index out of range Traceback (most recent call last): File "./get_gene_name.py", line 75, in main() File "./get_gene_name.py", line 72, in main add_gene_name(res_tmp_file, anno_file, output_file)
File "./get_gene_name.py", line 8, in add_gene_name result_tmp_data = read_TSV(result_tmp_file) File "/seq/RNASEQ/TOOLS/NCLscan/NCLscan_v1.4/utils.py", line 8, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: '0.result.tmp2' Traceback (most recent call last): File "./NCL_Scan5.py", line 30, in NCL_Scan5(pj_name) File "./NCL_Scan5.py", line 11, in NCL_Scan5 final_tmp = read_TSV("{PJ}.result.tmp3".format(PJ=pj_name)) File "/seq/RNASEQ/TOOLS/NCLscan/NCLscan_v1.4/utils.py", line 8, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: '0.result.tmp3' =========== Stop ============

Mon Feb 29 13:23:51 EST 2016

chiangtw commented 8 years ago

Please try the latest version(v1.6) of NCLscan.