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liumz93 / PEM-Q

a pipeline to process data of PEM-seq or data similar, which is more comprehensive than superQ
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IndexError: index 0 is out of bounds for axis 0 with size 0 #6

Open Mingdi-W opened 1 week ago

Mingdi-W commented 1 week ago

Hi, sir! When I run the example in the PEM-Q/data, I met this issue. Also, when I run my sample, I also met this problem. python 3.7.12 ######## 06 substitutions... ######## define_substitution.py CC055c 61986726 10 + [PEM-Q] basename: CC055c [PEM-Q] cutsite: 61986726 [PEM-Q] cutoff: 10 [PEM-Q] primer_strand: + Substitutions in cutsite +- cutoff: 0 0 Processing statistics... Traceback (most recent call last): File "/mnt/ZuoStorage3/wumingdi/soft/PEM-Q/main/define_substitution.py", line 181, in main() File "/mnt/ZuoStorage3/wumingdi/soft/PEM-Q/main/define_substitution.py", line 176, in main define_substitution(**kwargs) File "/mnt/ZuoStorage3/wumingdi/soft/PEM-Q/main/define_substitution.py", line 126, in define_substitution chrom = data["Bait_rname"][0] File "/mnt/ZuoStorage3/wumingdi/soft/miniconda/envs/PEM-Q/lib/python3.7/site-packages/pandas/core/series.py", line 939, in getitem return self._values[key] IndexError: index 0 is out of bounds for axis 0 with size 0

Mingdi-W commented 1 week ago

Also, nothing got in the results folder.

liumz93 commented 1 week ago

Hi Mingdi-W, if there’s nothing in the results folder, the error likely occurred in the earlier steps. The error you showed me is from step 06, but I believe that’s not the root cause. The IndexError may be due to an improperly generated file. Please check your log file for more details.