Execution error: EmptyDataError, No columns to parse from file
Ich hatte diesen Fehler schon mal gemailed, vor euerem letzten Hackathon, daher weiß ich nicht , ob es schon ein fix gab. Er tritt nicht immer auf, aber bei einem Run gehäuft.
$ QCumber-2 --input $path2reads --output $out_dir --threads 32
Provided cores: 32
Rules claiming more threads will be scaled down.
Job counts:
count jobs
25 fastqc_raw
1 run_all
1 write_batch_report
18 write_sample_json
19 write_sample_report
64
Job 152: Run FastQC on raw data.
Job 117: Write 11E02281_S13_L001.json
Job 160: Write 11E03025_S14_L001.json
Job 26: Write RL323_S20_L001.pdf
Job 170: Write 11E03068_S15_L001.json
Job 59: Write 11316-2_S30_L001.json
Job 266: Run FastQC on raw data.
Error in job write_sample_json while creating output files QCResults/_data/11316-2_S30_L001.json, QCResults/Classification/11316-2_S30_L001.kraken.png.
RuleException:
EmptyDataError in line 13 of /home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile:
No columns to parse from file
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/Snakefile", line 112, in __rule_write_sample_json
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 87, in get_fastqc_results
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 13, in createCSV
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 655, in parser_f
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 405, in _read
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 764, in __init__
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 985, in _make_engine
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 1605, in __init__
File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:6260)
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Error in job write_sample_json while creating output files QCResults/_data/11E02281_S13_L001.json, QCResults/Classification/11E02281_S13_L001.kraken.png.
RuleException:
EmptyDataError in line 13 of /home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile:
No columns to parse from file
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/Snakefile", line 112, in __rule_write_sample_json
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 87, in get_fastqc_results
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 13, in createCSV
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 655, in parser_f
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 405, in _read
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 764, in __init__
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 985, in _make_engine
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 1605, in __init__
File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:6260)
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Exiting because a job execution failed. Look above for error message
Exiting because a job execution failed. Look above for error message
Will exit after finishing currently running jobs.
Will exit after finishing currently running jobs.
Error in job write_sample_json while creating output files QCResults/_data/11E03068_S15_L001.json, QCResults/Classification/11E03068_S15_L001.kraken.png.
RuleException:
EmptyDataError in line 13 of /home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile:
No columns to parse from file
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/Snakefile", line 112, in __rule_write_sample_json
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 87, in get_fastqc_results
File "/home/DenekeC/anaconda3/envs/qcumber/opt/qcumber/modules/fastqc.snakefile", line 13, in createCSV
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 655, in parser_f
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 405, in _read
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 764, in __init__
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 985, in _make_engine
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/io/parsers.py", line 1605, in __init__
File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:6260)
File "/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Exiting because a job execution failed. Look above for error message
Will exit after finishing currently running jobs.
Removing temporary output file QCResults/FastQC/trimmed/RL323_S20_L001_R2_fastqc.
/home/DenekeC/anaconda3/envs/qcumber/lib/python3.6/site-packages/pandas/core/indexing.py:179: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame
See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
self._setitem_with_indexer(indexer, value)
Removing temporary output file QCResults/FastQC/raw/RL323_S20_L001_R1_fastqc.
Removing temporary output file QCResults/FastQC/raw/RL323_S20_L001_R2_fastqc.
Removing temporary output file QCResults/FastQC/trimmed/RL323_S20_L001_R1_fastqc.
Removing temporary output file QCResults/RL323_S20_L001.tex.
Removing temporary output file QCResults/RL323_S20_L001.aux.
Finished job 26.
1 of 64 steps (2%) done
Will exit after finishing currently running jobs.
Removing temporary output file QCResults/Trimmed/11E03025_S14_L001.trimmomatic.params.
Finished job 160.
2 of 64 steps (3%) done
Will exit after finishing currently running jobs.
Removing temporary output file QCResults/FastQC/raw/11463_S34_L001_R1_fastqc.html.
Finished job 152.
3 of 64 steps (5%) done
Will exit after finishing currently running jobs.
Removing temporary output file QCResults/FastQC/raw/11E01699_S10_L001_R1_fastqc.html.
Finished job 266.
4 of 64 steps (6%) done
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message