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.
I recently installed this tool for circular Rna detection But it is producing error. I am working with a plant sample. thus I prepared the gtf file from gff file (which was obtained from NCBI) using gffread. the error I am getting is as below:
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Read 0 genes, 0 transcripts and 138234 exons from the gtf file.
novoalign (V3.04.06 - Build May 18 2016 @ 16:23:46) - A short read aligner with qualities.
novoalign -r A 1 -t 0,1 -d output_tmp/tmp_NCLscan.JS2.ndx -f output_tmp/tmp_NCLscan.main.unmapped_1.fastq o
utput_tmp/tmp_NCLscan.main.unmapped_2.fastq --3Prime -o SAM
Starting at Fri Jul 29 10:25:03 2016
Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
Index Build Version: 3.4
Hash length: 6
Step size: 1
Paired Reads: 661919
Proper Pairs: 87 ( 0.0%)
Read Sequences: 1323838
Unique Alignment: 643 ( 0.0%)
Multi Mapped: 21 ( 0.0%)
No Mapping Found: 1323072 (99.9%)
QC Failures...
Homopolymer Filter: 102 ( 0.0%)
Elapsed Time: 16.659 (secs.)
CPU Time: 11.18 (min.)
Fragment Length Distribution
From To Count
105 119 2
120 134 2
135 149 4
150 164 6
165 179 7
180 194 2
195 209 2
210 224 3
225 239 6
240 254 9
255 269 10
270 284 8
285 299 15
300 314 4
315 329 0
330 344 3
345 359 1
360 374 0
375 389 0
390 404 3
Mean 244, Std Dev 65.1
Done at Fri Jul 29 10:25:20 2016
Start to split the input into 16 part ...
Time cost of split_file = 0.00453305244446 sec
Start to do the mp_blat using 16 processes ...
Time cost of mp_blat = 11.9849720001 sec
Merging results ...
Time cost of merge_result = 0.000910997390747 sec
Start to split the input into 16 part ...
Time cost of split_file = 0.00453400611877 sec
Start to do the mp_blat using 16 processes ...
Time cost of mp_blat = 1.68700289726 sec
Merging results ...
Time cost of merge_result = 0.00147986412048 sec
Start to split the input into 16 part ...
Time cost of split_file = 0.00458097457886 sec
Start to do the mp_blat using 16 processes ...
Time cost of mp_blat = 0.192430019379 sec
Merging results ...
Time cost of merge_result = 0.00123000144958 sec
Start to split the input into 16 part ...
Time cost of split_file = 0.00454807281494 sec
Start to do the mp_blat using 16 processes ...
Time cost of mp_blat = 0.0459880828857 sec
Merging results ...
Time cost of merge_result = 0.00110507011414 sec
Traceback (most recent call last):
File "/home/mjlabscis/Softwares/NCLscan-1.6/bin/get_gene_name.py", line 91, in
add_gene_name(args.result_tmp_file, args.gene_anno, args.output)
File "/home/mjlabscis/Softwares/NCLscan-1.6/bin/get_gene_name.py", line 26, in add_gene_name
result_tmp_data_with_gene_name.append(line_list + [','.join(gene_name_1), ','.join(gene_name_2), isIntragenic])
TypeError: sequence item 0: expected string, NoneType found
Traceback (most recent call last):
File "./NCLscan.py", line 448, in
NCL_Scan4(config, datasets_list, args.project_name, args.output_dir)
File "./NCLscan.py", line 255, in NCL_Scan4
final_tmp = read_TSV("{prefix}.result.tmp3".format(**config_options))
File "./NCLscan.py", line 279, in read_TSV
with open(tsv_file) as data_reader:
IOError: [Errno 2] No such file or directory: 'output_tmp/tmp_NCLscan.result.tmp3'
I had run tophat and another pipeline working on tophat output, produced no issues and I got a large number of circular Rnas.
But I also need to check it using this tool. Thus Kindly help me out.
I recently installed this tool for circular Rna detection But it is producing error. I am working with a plant sample. thus I prepared the gtf file from gff file (which was obtained from NCBI) using gffread. the error I am getting is as below: . . . . . Read 0 genes, 0 transcripts and 138234 exons from the gtf file.
novoalign (V3.04.06 - Build May 18 2016 @ 16:23:46) - A short read aligner with qualities.
(C) 2008-2015 Novocraft Technologies Sdn Bhd.
License file: /home/mjlabscis/Softwares/novocraft/novoalign.lic
Licensed to Jawaharlal Nehru University
novoalign -r A 1 -t 0,1 -d output_tmp/tmp_NCLscan.JS2.ndx -f output_tmp/tmp_NCLscan.main.unmapped_1.fastq o
utput_tmp/tmp_NCLscan.main.unmapped_2.fastq --3Prime -o SAM
Starting at Fri Jul 29 10:25:03 2016
Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
Index Build Version: 3.4
Hash length: 6
Step size: 1
Paired Reads: 661919
Proper Pairs: 87 ( 0.0%)
Read Sequences: 1323838
Unique Alignment: 643 ( 0.0%)
Multi Mapped: 21 ( 0.0%)
No Mapping Found: 1323072 (99.9%)
QC Failures...
Homopolymer Filter: 102 ( 0.0%)
Elapsed Time: 16.659 (secs.)
CPU Time: 11.18 (min.)
Fragment Length Distribution
From To Count
105 119 2
120 134 2
135 149 4
150 164 6
165 179 7
180 194 2
195 209 2
210 224 3
225 239 6
240 254 9
255 269 10
270 284 8
285 299 15
300 314 4
315 329 0
330 344 3
345 359 1
360 374 0
375 389 0
390 404 3
Mean 244, Std Dev 65.1
Done at Fri Jul 29 10:25:20 2016
Start to split the input into 16 part ... Time cost of split_file = 0.00453305244446 sec Start to do the mp_blat using 16 processes ... Time cost of mp_blat = 11.9849720001 sec Merging results ... Time cost of merge_result = 0.000910997390747 sec Start to split the input into 16 part ... Time cost of split_file = 0.00453400611877 sec Start to do the mp_blat using 16 processes ... Time cost of mp_blat = 1.68700289726 sec Merging results ... Time cost of merge_result = 0.00147986412048 sec Start to split the input into 16 part ... Time cost of split_file = 0.00458097457886 sec Start to do the mp_blat using 16 processes ... Time cost of mp_blat = 0.192430019379 sec Merging results ... Time cost of merge_result = 0.00123000144958 sec Start to split the input into 16 part ... Time cost of split_file = 0.00454807281494 sec Start to do the mp_blat using 16 processes ... Time cost of mp_blat = 0.0459880828857 sec Merging results ... Time cost of merge_result = 0.00110507011414 sec Traceback (most recent call last): File "/home/mjlabscis/Softwares/NCLscan-1.6/bin/get_gene_name.py", line 91, in
add_gene_name(args.result_tmp_file, args.gene_anno, args.output)
File "/home/mjlabscis/Softwares/NCLscan-1.6/bin/get_gene_name.py", line 26, in add_gene_name
result_tmp_data_with_gene_name.append(line_list + [','.join(gene_name_1), ','.join(gene_name_2), isIntragenic])
TypeError: sequence item 0: expected string, NoneType found
Traceback (most recent call last):
File "./NCLscan.py", line 448, in
NCL_Scan4(config, datasets_list, args.project_name, args.output_dir)
File "./NCLscan.py", line 255, in NCL_Scan4
final_tmp = read_TSV("{prefix}.result.tmp3".format(**config_options))
File "./NCLscan.py", line 279, in read_TSV
with open(tsv_file) as data_reader:
IOError: [Errno 2] No such file or directory: 'output_tmp/tmp_NCLscan.result.tmp3'
I had run tophat and another pipeline working on tophat output, produced no issues and I got a large number of circular Rnas. But I also need to check it using this tool. Thus Kindly help me out.