Hi, when I run this pipeline in a large cohort. I encountered some mistakes.
First, when I use pbs system to submit my jobs on one platform.
When this command filelines=cat ${INPUT_DISC}.breakpointINPUT.tsv is executed, it generates as many psl files as there are intervals. However, for certain intervals in some samples, a KeyError: 'pointGroup' error occurs during the calculation within these intervals, resulting in a corresponding reduction in the number of chromosome interval files obtained in the Breakpoints.tsv.
Eventually, I found that the occurrence of KeyError: 'pointGroup' is normal.
Seconed, when I use sbatch system to submit my jobs on another platform.
When I run this pipeline for the sample, I no longer encounter the KeyError: 'pointGroup' error. Instead, I am now facing several other errors that result in a reduced number of Breakpoints.tsv files, although the number of psl files remains the same as the number of intervals.
(1) ValueError: Shape of passed values is (7, 1), indices imply (7, 0)
Traceback (most recent call last):
/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py
(2) ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series
/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/common.py
ValueError: could not broadcast input array from shape (0,22) into shape (0)
ValueError: cannot copy sequence with size 22 to array axis with dimension 0
/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/frame.py
raise ValueError('Cannot set a frame with no defined index '
(3) ValueError: Shape of passed values is (6, 1), indices imply (6, 0)
/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py
(4) Write error to .psl
Finally, I found this error is caued by "No space left on device".
Do you know how to resolve this issue? Thank you in advance.
Hi, when I run this pipeline in a large cohort. I encountered some mistakes.
First, when I use pbs system to submit my jobs on one platform. When this command filelines=
cat ${INPUT_DISC}.breakpointINPUT.tsvis executed, it generates as many psl files as there are intervals. However, for certain intervals in some samples, a KeyError: 'pointGroup' error occurs during the calculation within these intervals, resulting in a corresponding reduction in the number of chromosome interval files obtained in the Breakpoints.tsv. Eventually, I found that the occurrence of KeyError: 'pointGroup' is normal.Seconed, when I use sbatch system to submit my jobs on another platform. When I run this pipeline for the sample, I no longer encounter the KeyError: 'pointGroup' error. Instead, I am now facing several other errors that result in a reduced number of Breakpoints.tsv files, although the number of psl files remains the same as the number of intervals. (1) ValueError: Shape of passed values is (7, 1), indices imply (7, 0) Traceback (most recent call last): /opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py (2) ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series /opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/common.py ValueError: could not broadcast input array from shape (0,22) into shape (0) ValueError: cannot copy sequence with size 22 to array axis with dimension 0 /opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/frame.py raise ValueError('Cannot set a frame with no defined index ' (3) ValueError: Shape of passed values is (6, 1), indices imply (6, 0) /opt/miniconda/envs/gatk/lib/python3.6/site-packages/pandas/core/internals.py (4) Write error to .psl Finally, I found this error is caued by "No space left on device".
Do you know how to resolve this issue? Thank you in advance.