Check $EXOME_TARGET is set in exome pipeline, more informative error message

[hdashnow]

The error below occurs when median_cov is 0. This can be caused by $EXOME_TARGET not being set, so the estimate is not restricted to the target region

• estimateSTR.py should produce informative error message when median_cov is 0.
• check $EXOME_TARGET is set at the start of the exome pipeline

======================================= Stage estimate_size ========================================

Processing 5 samples

Traceback (most recent call last):

  File "/exports/kg/programs/STRetch/scripts/estimateSTR.py", line 412, in <module>

    main()

  File "/exports/kg/programs/STRetch/scripts/estimateSTR.py", line 374, in main

    Y_pred = regr.predict(locus_totals['total_assigned_log'].values.reshape(-1, 1))

  File "/exports/kg/programs/STRetch/tools/miniconda/envs/STR/lib/python3.6/site-packages/sklearn/linear_model/base.py", line 256, in predict

    return self._decision_function(X)

  File "/exports/kg/programs/STRetch/tools/miniconda/envs/STR/lib/python3.6/site-packages/sklearn/linear_model/base.py", line 239, in _decision_function

    X = check_array(X, accept_sparse=['csr', 'csc', 'coo'])

  File "/exports/kg/programs/STRetch/tools/miniconda/envs/STR/lib/python3.6/site-packages/sklearn/utils/validation.py", line 453, in check_array

    _assert_all_finite(array)

  File "/exports/kg/programs/STRetch/tools/miniconda/envs/STR/lib/python3.6/site-packages/sklearn/utils/validation.py", line 44, in _assert_all_finite

    " or a value too large for %r." % X.dtype)

ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

ERROR: Command failed with exit status = 1 :

 

PATH=$PATH:/exports/kg/programs/STRetch/tools/bin; /exports/kg/programs/STRetch/tools/bin/python /exports/kg/programs/STRetch/scripts/estimateSTR.py --locus_counts /exports/kg/programs/STRetch/test/11.locus_counts /exports/kg/programs/STRetch/test/1.locus_counts /exports/kg/programs/STRetch/test/49.locus_counts /exports/kg/programs/STRetch/test/54.locus_counts /exports/kg/programs/STRetch/test/69.locus_counts  --STR_counts 11.STR_counts 1.STR_counts 49.STR_counts 54.STR_counts 69.STR_counts  --median_cov 11.median_cov 1.median_cov 49.median_cov 54.median_cov 69.median_cov --model /exports/kg/programs/STRetch/scripts/STRcov.model.csv --control /exports/kg/programs/STRetch/reference-data/PCRfreeWGS.controls.tsv

 

 

========================================= Pipeline Failed ==========================================

 

Command failed with exit status = 1 :

 

PATH=$PATH:/exports/kg/programs/STRetch/tools/bin; /exports/kg/programs/STRetch/tools/bin/python /exports/kg/programs/STRetch/scripts/estimateSTR.py --locus_counts /exports/kg/programs/STRetch/test/11.locus_counts /exports/kg/programs/STRetch/test/1.locus_counts /exports/kg/programs/STRetch/test/49.locus_counts /exports/kg/programs/STRetch/test/54.locus_counts /exports/kg/programs/STRetch/test/69.locus_counts  --STR_counts 11.STR_counts 1.STR_counts 49.STR_counts 54.STR_counts 69.STR_counts  --median_cov 11.median_cov 1.median_cov 49.median_cov 54.median_cov 69.median_cov --model /exports/kg/programs/STRetch/scripts/STRcov.model.csv --control /exports/kg/programs/STRetch/reference-data/PCRfreeWGS.controls.tsv

 

Use 'bpipe errors' to see output from failed commands.