multiqc / multiqc_bcbio Goto Github PK
View Code? Open in Web Editor NEWMultiQC plugin for bcbio_nextgen pipeline
License: MIT License
multiqc_bcbio's Issues
Add 50 genes panel to get always the same coverage based metrics
Add table section with all metrics
not only some at the top, but the full information from bcbio run
fix ylab in completeness report
it changes every time we move to another cutoff. need to use ylab: whatever inside the config dict.
list length check needed
MultiQC_bcbio/multiqc_bcbio/srna.py
Line 36 in 6d532ab
I'm getting errors running this module within bcbio. A simple if (len(cols) > 0): on the previous line fixes it.
MultiQC module fails with bcbio_vm
I ran bcbio_vm on one sample on one machine (bcbio_vm.py run -n 15 ../config/samples.yaml) but got the following error at the multiqc stage. Any help greatly appreciated, thanks.
[2018-03-07T08:04Z] summarize metrics
[2018-03-07T08:04Z] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export PATH=/usr/local/share/bcbio-nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio-nextgen/anaconda/bin/multiqc -f -l /mnt/work/qc/multiqc/list_files.tx
t -o /mnt/work/bcbiotx/tmpu8rvWt
[INFO ] multiqc : This is MultiQC v1.4
[INFO ] multiqc : Template : default
Searching 20 files..
[INFO ] goleft_indexcov : Found goleft indexcov ROC reports for 1 samples
[INFO ] goleft_indexcov : Found goleft indexcov bin reports for 1 samples
[INFO ] bcbio : Found 1 reports
[ERROR ] multiqc : Oops! The 'bcbio' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
If possible, please include a log file that triggers the error - the last file found was:
/mnt/work/qc/multiqc/report/metrics/target_info.yaml
============================================================
Module bcbio raised an exception: Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/bin/multiqc", line 427, in multiqc
output = mod()
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/multiqc_bcbio/bcbio.py", line 111, in __init__
if "coverage_avg_chart" in coverage_avg_plot:
TypeError: argument of type 'NoneType' is not iterable
============================================================
[INFO ] samtools : Found 1 stats reports
[INFO ] samtools : Found 1 idxstats reports
[INFO ] bcftools : Found 1 stats reports
[INFO ] snpeff : Found 1 reports
[INFO ] fastqc : Found 1 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : ../../bcbiotx/tmpu8rvWt/multiqc_report.html
[INFO ] multiqc : Data : ../../bcbiotx/tmpu8rvWt/multiqc_data
[INFO ] multiqc : MultiQC complete
' returned non-zero exit status 1
Uncaught exception occurred
Traceback (most recent call last):
File "/home/ubuntu/projects/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/home/ubuntu/projects/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'docker attach --no-stdin 893c59ed13112855586eb83f0c287f6591dc431711474501b296d5cfa87f657b
_do_run(cmd, checks, log_stdout, env=env)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export PATH=/usr/local/share/bcbio-nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio-nextgen/anaconda/bin/multiqc -f -l /mnt/work/qc/multiqc/list_files.txt -o /mnt/work/bcbiotx/tmpu8rvWt
[INFO ] multiqc : This is MultiQC v1.4
[INFO ] multiqc : Template : default
Searching 20 files..
[INFO ] goleft_indexcov : Found goleft indexcov ROC reports for 1 samples
[INFO ] goleft_indexcov : Found goleft indexcov bin reports for 1 samples
[INFO ] bcbio : Found 1 reports
[ERROR ] multiqc : Oops! The 'bcbio' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
If possible, please include a log file that triggers the error - the last file found was:
/mnt/work/qc/multiqc/report/metrics/target_info.yaml
============================================================
Module bcbio raised an exception: Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/bin/multiqc", line 427, in multiqc
output = mod()
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/multiqc_bcbio/bcbio.py", line 111, in __init__
if "coverage_avg_chart" in coverage_avg_plot:
TypeError: argument of type 'NoneType' is not iterable
============================================================
[INFO ] samtools : Found 1 stats reports
[INFO ] samtools : Found 1 idxstats reports
[INFO ] bcftools : Found 1 stats reports
[INFO ] snpeff : Found 1 reports
[INFO ] fastqc : Found 1 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : ../../bcbiotx/tmpu8rvWt/multiqc_report.html
[INFO ] multiqc : Data : ../../bcbiotx/tmpu8rvWt/multiqc_data
[INFO ] multiqc : MultiQC complete
' returned non-zero exit status 1
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 241, in <module>
main(**kwargs)
File "/usr/local/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 186, in variant2pipeline
samples = qcsummary.generate_parallel(samples, run_parallel)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py", line 38, in generate_parallel
samples = run_parallel("multiqc_summary", [samples])
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"], batch_size=1)(joblib.delayed(fn)(x) for x in items):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 779, in __call__
while self.dispatch_one_batch(iterator):
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 625, in dispatch_one_batch
self._dispatch(tasks)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 588, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 111, in apply_async
result = ImmediateResult(func)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 332, in __init__
self.results = batch()
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 131, in __call__
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 52, in wrapper
return apply(f, *args, **kwargs)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 207, in multiqc_summary
return multiqc.summary(*args)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/qc/multiqc.py", line 62, in summary
do.run(cmd.format(**locals()), "Run multiqc")
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; export PATH=/usr/local/share/bcbio-nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio-nextgen/anaconda/bin/multiqc -f -l /mnt/work/qc/multiqc/list_files.txt -o /mnt/work/bcbiotx/tmpu8rvWt
[INFO ] multiqc : This is MultiQC v1.4
[INFO ] multiqc : Template : default
Searching 20 files..
[INFO ] goleft_indexcov : Found goleft indexcov ROC reports for 1 samples
[INFO ] goleft_indexcov : Found goleft indexcov bin reports for 1 samples
[INFO ] bcbio : Found 1 reports
[ERROR ] multiqc : Oops! The 'bcbio' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
If possible, please include a log file that triggers the error - the last file found was:
/mnt/work/qc/multiqc/report/metrics/target_info.yaml
============================================================
Module bcbio raised an exception: Traceback (most recent call last):
File "/usr/local/share/bcbio-nextgen/anaconda/bin/multiqc", line 427, in multiqc
output = mod()
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/multiqc_bcbio/bcbio.py", line 111, in __init__
if "coverage_avg_chart" in coverage_avg_plot:
TypeError: argument of type 'NoneType' is not iterable
============================================================
[INFO ] samtools : Found 1 stats reports
[INFO ] samtools : Found 1 idxstats reports
[INFO ] bcftools : Found 1 stats reports
[INFO ] snpeff : Found 1 reports
[INFO ] fastqc : Found 1 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : ../../bcbiotx/tmpu8rvWt/multiqc_report.html
[INFO ] multiqc : Data : ../../bcbiotx/tmpu8rvWt/multiqc_data
[INFO ] multiqc : MultiQC complete
' returned non-zero exit status 1
' returned non-zero exit status 1
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