There are no main datasets assigned.

[kopardev]

I am getting this error

/data/Ziegelbauer_lab/tools/NCLscan-1.7.0/NCLscan.py -c /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/nclscan.config -o test -pj iSLK-BAC16_Uninduced_R2 --fq1 /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/results/iSLK-BAC16_Uninduced_R2/trim/iSLK-BAC16_Uninduced_R2.R1.trim.fastq.gz --fq2 /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/results/iSLK-BAC16_Uninduced_R2/trim/iSLK-BAC16_Uninduced_R2.R2.trim.fastq.gz
There are no main datasets assigned.

Any idea? Here is the config file

#############################
### NCLscan Configuration ###

## The directory of references and indices
## The script "create_reference.py" would create the needed references and indices here.
NCLscan_ref_dir = /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/NCLscan_index


## The following four reference files can be downloaded from the GENCODE website (http://www.gencodegenes.org/).

## The reference genome sequence, eg. /path/to/GRCh37.p13.genome.fa
Reference_genome = /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/ref.fa

## The gene annotation file, eg. /path/to/gencode.v19.annotation.gtf
Gene_annotation = /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/ref.fixed.gtf

## The protein-coding transcript sequences, eg. /path/to/gencode.v19.pc_transcripts.fa
Protein_coding_transcripts = /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/ref.transcripts.fa

## The long non-coding RNA transcript sequences, eg. /path/to/gencode.v19.lncRNA_transcripts.fa
lncRNA_transcripts = /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/ref.dummy.fa


## External tools
## these are set to "module load" on BIOWULF

bedtools_bin      = /usr/local/apps/bedtools/2.29.0/bin/bedtools
blat_bin          = /usr/local/apps/blat/3.5/blat
bwa_bin           = /usr/local/apps/bwa/0.7.17/bwa
samtools_bin      = /usr/local/apps/samtools/1.15.1/bin/samtools
novoalign_bin     = /usr/local/apps/novocraft/4.03.05/novoalign
novoindex_bin     = /usr/local/apps/novocraft/4.03.05/novoindex


## Bin
NCLscan_bin = {NCLscan_dir}/bin

Add_read_count_bin      = {NCLscan_bin}/Add_read_count.py
AssembleExons_bin       = {NCLscan_bin}/AssembleExons
AssembleFastq_bin       = {NCLscan_bin}/AssembleFastq
AssembleJSeq_bin        = {NCLscan_bin}/AssembleJSeq.py
append_Z3_tag           = {NCLscan_bin}/append_Z3_tag.py
FastqOut_bin            = {NCLscan_bin}/FastqOut
get_gene_name_bin       = {NCLscan_bin}/get_gene_name.py
GetInfo_bin             = {NCLscan_bin}/GetInfo
GetKey_bin              = {NCLscan_bin}/GetKey
GetNameB4Dot_bin        = {NCLscan_bin}/GetNameB4Dot
InsertInList_bin        = {NCLscan_bin}/InsertInList
JSFilter_bin            = {NCLscan_bin}/JSFilter
JSParser_bin            = {NCLscan_bin}/JSParser
JunctionSite2BED_bin    = {NCLscan_bin}/JunctionSite2BED
mp_blat_bin             = {NCLscan_bin}/mp_blat.py
PslChimeraFilter_bin    = {NCLscan_bin}/PslChimeraFilter
RemoveInList_bin        = {NCLscan_bin}/RemoveInList
RetainInList_bin        = {NCLscan_bin}/RetainInList
RmBadMapping_bin        = {NCLscan_bin}/RmBadMapping
RmColinearPairInSam_bin = {NCLscan_bin}/RmColinearPairInSam
RmRedundance_bin        = {NCLscan_bin}/RmRedundance
SeqOut_bin              = {NCLscan_bin}/SeqOut



###########################
### Advanced parameters ###
###########################

## The following two parameters indicate the maximal read length (L) and fragment size of the used paired-end RNA-seq data (FASTQ files), where fragment size = 2L + insert size.
## If L > 151, the users should change these two parameters to (L, 2L + insert size).
max_read_len      = 151
max_fragment_size = 500


## The base quality threshold. The value should be a non-negative integer.
quality_score = 20

## The collection of the supporting reads must span the NCL junction boundary by the setting size of span range on both sides of the junction site.
span_range = 50


###################
### Performance ###
###################

## Parameters for bwa mem
## The number of threads
bwa-mem-t = 56

## Parameters for mp_blat.py
## The number of processes for running blat
##
## NOTE: The memory usage of each blat process would be up to 4 GB!
##
mp_blat_process = 56

[chiangtw]

Hi,

Could you provide me the information about the operating system and the version of python?
Thank you!

tw