Error message in the processing of MutPredMerge (exactly MutPred2.0)

[minn333]

Dear author:
I encountered error message in the processing of MutPredMerge. It is the same problem while i am running MutPred2.0 alone too, however i could get the output file despite of error while runnig standalone version. Do you have any suggestion? Thanks.

Select jobs to execute...
Initializing ...
Initializing ...
Initializing ...
Initializing ...
ANNOVAR input format detected. Converting ...
ANNOVAR input format detected. Converting ...
ANNOVAR input format detected. Converting ...
ANNOVAR input format detected. Converting ...
After merging identical sequences, 4 unique substitutions in 2 sequences were found.
Predicting ...
After merging identical sequences, 4 unique substitutions in 2 sequences were found.
Predicting ...
After merging identical sequences, 4 unique substitutions in 3 sequences were found.
Predicting ...
After merging identical sequences, 4 unique substitutions in 3 sequences were found.
Predicting ...
Warning: No match found in database. Returning empty string.

In get_alignment (line 47)
In make_feature_matrix (line 149)
In mutpred2 (line 108)
Warning: No match found in database. Returning empty array.
In get_cindex (line 47)
In make_feature_matrix (line 152)
In mutpred2 (line 108)
Finished 1 of 3 sequences
Finished 1 of 2 sequences
Finished 1 of 2 sequences
Warning: No match found in database. Returning empty matrix.
In get_pssm (line 44)
In make_feature_matrix (line 108)
In mutpred2 (line 108)
[blastpgp] WARNING: Unable to open BLOSUM62
[blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
[blastpgp] WARNING: SetUpBlastSearch failed.
/bin/bash: line 1: 200265 Segmentation fault (core dumped) /$PATH/MutPredMerge-master/tools/mutpred2.0/blast-2.2.18/bin/blastpgp -i /$PATH/MutPredMerge-master/tools/mutpred2.0/tp901e5a8b_0f18_43d8_9054_0052dc84ffad.faa -d /$PATH/MutPredMerge-master/tools/mutpred2.0/nr062813/nr -Q tp901e5a8b_0f18_43d8_9054_0052dc84ffad.pssm -a 3 -h 0.0001 -j 3 > /dev/null
/$PATH/MutPredMerge-master/tools/mutpred2.0/blast-2.2.18/bin/blastpgp -i /$PATH/MutPredMerge-master/tools/mutpred2.0/tp901e5a8b_0f18_43d8_9054_0052dc84ffad.faa -d /$PATH/MutPredMerge-master/tools/mutpred2.0/nr062813/nr -Q tp901e5a8b_0f18_43d8_9054_0052dc84ffad.pssm -a 3 -h 0.0001 -j 3 > /dev/null: Segmentation fault
Error using PSSMread (line 4)
file tp901e5a8b_0f18_43d8_9054_0052dc84ffad.pssm doesn't exist!!!

Error in make_feature_matrix (line 122)

Error in mutpred2 (line 108)

[Thu Jun 9 10:39:56 2022]
Error in rule MutPred2:
jobid: 22
output: /$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_3_output.txt
shell:
cd tools/mutpred2.0 && ./run_mutpred2.sh -i /$PATH/MutPredMerge-master/intermediates/faa/20220107_bwamem.missense_3.faa -p 1 -c 1 -b 0 -t 0.05 -f 2 -o /$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_3_output.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job MutPred2 since they might be corrupted:
/$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_3_output.txt
Finished 2 of 2 sequences
[Thu Jun 9 10:40:28 2022]
Finished job 20.
4 of 20 steps (20%) done
Finished 2 of 3 sequences
Finished 3 of 3 sequences
[Thu Jun 9 10:45:24 2022]
Finished job 23.
5 of 20 steps (25%) done
Finished 1 of 3 sequences
Warning: No match found in database. Returning empty matrix.

In get_pssm (line 44)
In make_feature_matrix (line 108)
In mutpred2 (line 108)
[blastpgp] WARNING: Unable to open BLOSUM62
[blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
[blastpgp] WARNING: SetUpBlastSearch failed.
/bin/bash: line 1: 228741 Segmentation fault (core dumped) /$PATH/MutPredMerge-master/tools/mutpred2.0/blast-2.2.18/bin/blastpgp -i /$PATH/MutPredMerge-master/tools/mutpred2.0/tp12a9c409_7d8a_43e3_a41b_65bce037296c.faa -d /work/genegogo2019/MutPredMerge-master/tools/mutpred2.0/nr062813/nr -Q tp12a9c409_7d8a_43e3_a41b_65bce037296c.pssm -a 3 -h 0.0001 -j 3 > /dev/null
/$PATH/MutPredMerge-master/tools/mutpred2.0/blast-2.2.18/bin/blastpgp -i /$PATH/MutPredMerge-master/tools/mutpred2.0/tp12a9c409_7d8a_43e3_a41b_65bce037296c.faa -d /$PATH/MutPredMerge-master/tools/mutpred2.0/nr062813/nr -Q tp12a9c409_7d8a_43e3_a41b_65bce037296c.pssm -a 3 -h 0.0001 -j 3 > /dev/null: Segmentation fault
Error using PSSMread (line 4)
file tp12a9c409_7d8a_43e3_a41b_65bce037296c.pssm doesn't exist!!!

Error in make_feature_matrix (line 122)

Error in mutpred2 (line 108)

---

log file as below###

Select jobs to execute...
[Thu Jun 9 10:39:56 2022]
Error in rule MutPred2:
jobid: 22
output: /$PATH/MutPredMerge-master/intermediates/scores/TAAD0198_20220107_bwamem.missense_3_output.txt
shell:
cd tools/mutpred2.0 && ./run_mutpred2.sh -i /$PATH/MutPredMerge-master/intermediates/faa/20220107_bwamem.missense_3.faa -p 1 -c 1 -b 0 -t 0.05 -f 2 -o /$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_3_output.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job MutPred2 since they might be corrupted:
/$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_3_output.txt
[Thu Jun 9 10:40:28 2022]
Finished job 20.
4 of 20 steps (20%) done
[Thu Jun 9 10:45:24 2022]
Finished job 23.
5 of 20 steps (25%) done
[Thu Jun 9 10:47:07 2022]
Error in rule MutPred2:
jobid: 19
output: /$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_0_output.txt
shell:
cd tools/mutpred2.0 && ./run_mutpred2.sh -i /$PATH/MutPredMerge-master/intermediates/faa/20220107_bwamem.missense_0.faa -p 1 -c 1 -b 0 -t 0.05 -f 2 -o /$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_0_output.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job MutPred2 since they might be corrupted:
/$PATH/MutPredMerge-master/intermediates/scores/20220107_bwamem.missense_0_output.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-06-09T103601.955196.snakemake.log