Comments (3)
Hi,
I had the same problem when I am running DaPars_main.py.
[Wed 12 Jan 2022 04:37:58 PM ] Start Analysis ...
[Wed 12 Jan 2022 04:37:58 PM ] Loading coverage ...
Traceback (most recent call last):
File "/sw/QFAB/miniconda3/envs/dapars_0.9.1/dapars/src/DaPars_main.py", line 549, in
De_Novo_3UTR_Identification_Loading_Target_Wig_for_TCGA_Multiple_Samples_Main(sys.argv)
File "/sw/QFAB/miniconda3/envs/dapars_0.9.1/dapars/src/DaPars_main.py", line 155, in De_Novo_3UTR_Identification_Loading_Target_Wig_for_TCGA_Multiple_Samples_Main
All_samples_Target_3UTR_coverages, All_samples_sequencing_depths, UTR_events_dict = Load_Target_Wig_files(All_Sample_files, Annotated_3UTR_file)
File "/sw/QFAB/miniconda3/envs/dapars_0.9.1/dapars/src/DaPars_main.py", line 499, in Load_Target_Wig_files
region_start = int(fields[1])
IndexError: list index out of range
my extracted_3UTR.bed is like
chr5 100589900 100592136 ENSMUST00000239512.1|Lin54|chr5|- 0 -
chr17 37314356 37314706 ENSMUST00000174016.8|Zfp57|chr17|+ 0 +
chr15 79173371 79173485 ENSMUST00000174375.2|Pla2g6|chr15|- 0 -
wig file is like
chr1 0 3191839 0
chr1 3191839 3191841 1
chr1 3191841 3191929 2
chr1 3191929 3192634 0
Can anyone give some suggestions?
Thanks
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from dapars.
I had the same problem when I am running DaPars2_Multi_Sample_Multi_Chr.py
Traceback (most recent call last):
File "/gss1/home/dmt20191202/conda/biosoft/dapars2/src/DaPars2_Multi_Sample_Multi_Chr.py", line 449, in
De_Novo_3UTR_Identification_Loading_Target_Wig_for_TCGA_Multiple_Samples_Multiple_threads_Main3_shared_list(sys.argv)
File "/gss1/home/dmt20191202/conda/biosoft/dapars2/src/DaPars2_Multi_Sample_Multi_Chr.py", line 110, in De_Novo_3UTR_Identification_Loading_Target_Wig_for_TCGA_Multiple_Samples_Multiple_threads_Main3_shared_list
fh=open(sys.argv[2],'r')
IndexError: list index out of range
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Related Issues (18)
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- Dapars generate divide by zero issue HOT 2
- Can not run Dapars: ImportError: cannot import name entr HOT 1
- DaPars does not handle scientific notation in the wig file coverage field (field 4) HOT 1
- Only outputting 100 UTRs
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- hg19_4_19_2012_Refseq_id_from_UCSC.txt HOT 1
- Migrate to Python 3 HOT 5
- Chrom name issue HOT 2
- does dapars support strand-specific RNA-Seq? HOT 1
- Possible to install using conda? HOT 2
- Docs link broken? HOT 3
- DaPars_Extract_Anno.py - coordinates in output BED file (and 'Loci' column) are shifted 1 nucleotide from source transcript
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