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hillerlab / TFforge

Identifying transcription factors involved in phenotypic differences between species
MIT License
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test error #2

Open aaannaw opened 1 month ago

aaannaw commented 1 month ago

Dear author, I am running the example data: REforge.py data/tree_simulation.nwk data/motifs.wtmx data/species_lost_simulation.txt elements_simul.ls --windowsize 200 --scorefile scores_simulation -bg=background; bash alljobs_scores_simulation > scores_simulation. However, I got the warning: 

WARNING:root:Error in score_sequence_with_stubb: Command 'stubb_noPseudoCount AGTGGTAGTAGGCTGTCAAGGCAATATGAGGACATTCGGGACCGTTGTCGGACTCCCGCCTGTACGGAGCTCGACTGGAGTTAGGGAGCATCAAGATATAAATTCAGGATCACTCTGAACCTATGAATGGAGCTTAGAAGCGGCACATGATCGAGTCTTCGTAAATCTAGGCCAGCGTTAAAGTTCAGTGCGTCTCACTGG data/motifs.wtmx 200.0 1  -b /data/01/p1/user157/software/REforge/example/background//gc0.49/gc0.49.fa -brief -seq' died with <Signals.SIGKILL: 9>.
WARNING:root:Error in score_sequence_with_stubb: Command 'stubb_noPseudoCount ACGGATCGCATTCCCATCTCCGGACTGCATTATTCGAACGCCGGGTATGGTATATATGTAGGGCTATGGGGAAATTTGAGATAAGGACAGGGGATTAGCCTGCACCGTGTTAAACATGGTCAGGAAACCAGGTACGTCGGCATACGTCCAATCATATTGCAAGTAGCTTGAACAAGTAGGCCACGTCGGTTTTGGGGCCGA data/motifs.wtmx 200.0 1  -b /data/01/p1/user157/software/REforge/example/background//gc0.49/gc0.49.fa -brief -seq' died with <Signals.SIGKILL: 9>.

The result file scores_simulation is abnormal: image

Additionally, I noticed the similar error in the link [https://github.com/hillerlab/REforge/issues/4]. I think maybe the error is due to stubb program and the directory /data/01/p1/user157/software/stubb_2.1/bin only include stubb_fitprobs_noPseudoCount, stubb_fixedprobs_noPseudoCount and stubb_noPseudoCount, not stubb stubb_fitprobs stubb_fixedprobs stubbh01 stubbh01f stubbms stubbms_modifyalignments

I try all ways in the https://github.com/hillerlab/REforge/issues, but did not work.

Could you give me any suggestions? Looking forward with your reply. Best wishes! Na Wan

MichaelHiller commented 1 month ago

Thx for reporting this. I'll ping Bjoern, who can hopefully help here.