problem with -- list index out of range

[sunhaifeng123]

Hi :
I'm using Dapars to find APA,but some problems seem to fused me :
python /home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py -b $refbed -s $genesymbol -o Dapars_extracted_3UTR.bed

Generating regions ...
Traceback (most recent call last):
File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 151, in
Extract_Anno_main(sys.argv[1:])
File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 139, in Extract_Anno_main
Annotation_prepar_3UTR_extraction(gene_bed_file, gene_symbol_annotation_file,output_extract_file)
File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 17, in Annotation_prepar_3UTR_extraction
gene_symbol = fields[1]
IndexError: list index out of range

do u know what's happened ? how should i solve this problem?
Thanks very much !

Haifeng Sun
China Nanjing Medical University

[obenno]

Hi Sun, Is your gene symbol file properly formatted? Could you provide some example lines? Bests, Zhixia

…

On Sat, Nov 17, 2018 at 1:36 PM sunhaifeng123 ***@***.***> wrote: Hi : I'm using Dapars to find APA,but some problems seem to fused me : python /home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py -b $refbed -s $genesymbol -o Dapars_extracted_3UTR.bed Generating regions ... Traceback (most recent call last): File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 151, in Extract_Anno_main(sys.argv[1:]) File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 139, in Extract_Anno_main Annotation_prepar_3UTR_extraction(gene_bed_file, gene_symbol_annotation_file,output_extract_file) File "/home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py", line 17, in Annotation_prepar_3UTR_extraction gene_symbol = fields[1] IndexError: list index out of range do u know what's happened ? how should i solve this problem? Thanks very much ! Haifeng Sun China Nanjing Medical University — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF1oxHYdETeMTpIFDsiwU36ZdobMz0_oks5uv6BAgaJpZM4YnSgs> .

[mick42-star]

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

[MTDeng]

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