The hyphy command failed. Not sure why since temporary input files are not kept.
Here is my command:
python BAD_Mutations.py -v DEBUG \
predict \
-c BAD_Mutations_Config.txt \
-f test.fasta \
-s subs.txt
My guess is that hyphy needs alignment to be cleaned up, remove characters from names, remove bootstrap values - which I previously did for Barley before running hyphy.
===2015-11-10 12:35:02,225 - LRT_Predict===
INFO Nucleotide alignment in /tmp/BAD_Mutations_BackTranslated_9rv1TH.fasta
===2015-11-10 12:35:02,225 - LRT_Predict===
INFO Tree in /tmp/pastajob_1447180465.400478.tre
===2015-11-10 12:35:02,226 - LRT_Prediction===
DEBUG Checking if subs.txt exists.
===2015-11-10 12:35:02,226 - LRT_Prediction===
WARNING Variant on line 1 of input file subs.txt does not have an ID. Using the empty string ('') as an ID.
===2015-11-10 12:35:02,226 - LRT_Prediction===
WARNING Variant on line 2 of input file subs.txt does not have an ID. Using the empty string ('') as an ID.
===2015-11-10 12:35:02,226 - LRT_Prediction===
INFO Input file subs.txt contains 2 positions to predict.
===2015-11-10 12:35:02,228 - LRT_Prediction===
DEBUG test is at position 12
===2015-11-10 12:35:02,229 - LRT_Prediction===
DEBUG bash /media/jfay/data1/projects/barley/BAD_Mutations/Shell_Scripts/Prediction.sh /usr/local/bin/HYPHYSP /media/jfay/data1/projects/barley/BAD_Mutations/Shell_Scripts/LRT.hyphy /tmp/BAD_Mutations_HYHPY_In_kGLw8c.txt /tmp/BAD_Mutations_HYPHY_Out_IuvmhL.txt
===2015-11-10 12:35:02,298 - LRT_Prediction===
DEBUG stdout:
The hyphy command failed. Not sure why since temporary input files are not kept.
Here is my command: python BAD_Mutations.py -v DEBUG \ predict \ -c BAD_Mutations_Config.txt \ -f test.fasta \ -s subs.txt
My guess is that hyphy needs alignment to be cleaned up, remove characters from names, remove bootstrap values - which I previously did for Barley before running hyphy.
Here is the error:
PASTA INFO: Total time spent: 36.7152650356s
===2015-11-10 12:35:02,202 - LRT_Predict=== DEBUG stderr:
===2015-11-10 12:35:02,225 - LRT_Predict=== INFO Nucleotide alignment in /tmp/BAD_Mutations_BackTranslated_9rv1TH.fasta ===2015-11-10 12:35:02,225 - LRT_Predict=== INFO Tree in /tmp/pastajob_1447180465.400478.tre ===2015-11-10 12:35:02,226 - LRT_Prediction=== DEBUG Checking if subs.txt exists. ===2015-11-10 12:35:02,226 - LRT_Prediction=== WARNING Variant on line 1 of input file subs.txt does not have an ID. Using the empty string ('') as an ID. ===2015-11-10 12:35:02,226 - LRT_Prediction=== WARNING Variant on line 2 of input file subs.txt does not have an ID. Using the empty string ('') as an ID. ===2015-11-10 12:35:02,226 - LRT_Prediction=== INFO Input file subs.txt contains 2 positions to predict. ===2015-11-10 12:35:02,228 - LRT_Prediction=== DEBUG test is at position 12 ===2015-11-10 12:35:02,229 - LRT_Prediction=== DEBUG bash /media/jfay/data1/projects/barley/BAD_Mutations/Shell_Scripts/Prediction.sh /usr/local/bin/HYPHYSP /media/jfay/data1/projects/barley/BAD_Mutations/Shell_Scripts/LRT.hyphy /tmp/BAD_Mutations_HYHPY_In_kGLw8c.txt /tmp/BAD_Mutations_HYPHY_Out_IuvmhL.txt ===2015-11-10 12:35:02,298 - LRT_Prediction=== DEBUG stdout:
===2015-11-10 12:35:02,298 - LRT_Prediction=== DEBUG stderr: /media/jfay/data1/projects/barley/BAD_Mutations/Shell_Scripts/Prediction.sh: line 15: 14577 Segmentation fault ${HYPHY} ${PREDICTION_SCRIPT} <<< ${INPUT} > ${OUTPUT}
===2015-11-10 12:35:02,298 - LRT_Predict=== INFO Prediction in /media/jfay/data1/projects/barley/BAD_Mutations/test_Predictions.txt