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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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TypeError when Running CLEAR: 'NoneType' object is not iterable #18

Open JerryZhang-1222 opened 3 years ago

JerryZhang-1222 commented 3 years ago

hello! First thanks a lot for providing a fantanstic tool for circRNA analysis! I have an issue when running circ_quant, the nohup.out file says that: TypeError: 'NoneType' object is not iterable.

Here is the log file:

Parameters:

Namespace(bam='/home/zhangfy/data_projects/RNAseq/LW_MPP/sambamfiles/C-1.sam.sorted.bam', circ='/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/C-1_circularRNA_known.txt', length=False, output='C-1_quant.txt', ratio=1, ref='/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/Rattus.genepred', threshold=1, tmp=True)

Parameters

genePredToGtf is required for maximal isoform selection!

Parameters:

Namespace(bam='/home/zhangfy/data_projects/RNAseq/LW_MPP/sambamfiles/C-1.sam.sorted.bam', circ='/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/C-1_circularRNA_known.txt', length=False, output='C-1_quant.txt', ratio=1, ref='/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/Rattus.genepred', threshold=1, tmp=True)

Parameters

Traceback (most recent call last): File "/home/zhangfy/miniconda3/envs/RNAseq/bin/circ_quant", line 11, in load_entry_point('CLEAR==1.0.1', 'console_scripts', 'circ_quant')() File "/home/zhangfy/miniconda3/envs/RNAseq/lib/python3.6/site-packages/CLEAR-1.0.1-py3.6.egg/src/circ_quant.py", line 334, in main spReads.extract(extract_args) File "/home/zhangfy/miniconda3/envs/RNAseq/lib/python3.6/site-packages/CLEAR-1.0.1-py3.6.egg/src/spReads.py", line 83, in extract cigar = getCigar(read) File "/home/zhangfy/miniconda3/envs/RNAseq/lib/python3.6/site-packages/CLEAR-1.0.1-py3.6.egg/src/spReads.py", line 30, in getCigar cigar = [ (num2op[num], length) for num, length in read.cigartuples] TypeError: 'NoneType' object is not iterable

And this is my code:

nohup circ_quant -c /home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/C-1_circularRNA_known.txt \
-b /home/zhangfy/data_projects/RNAseq/LW_MPP/sambamfiles/C-1.sam.sorted.bam \
-t \
-r /home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/Rattus.genepred \
-o C-1_quant.txt &

C-1_circularRNA_known.txt is the output file of CIRCExplorer2 annotate C-1.sam.sorted.bam is the bam file of one sample. I have used samtools sort and samtools index to get this bam file Rattus.genepred is the genepred file

Thanks a lot! Zhangfy

JerryZhang-1222 commented 3 years ago

also, I have installed genePredToGtf but it still told me that "genePredToGtf is required for maximal isoform selection!". I'm quite confused. Thanks!