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MicrobeLab / DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep learning
https://doi.org/10.1093/nargab/lqaa009
Apache License 2.0
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Error: seq-shuf not detected #12

Open mrumi opened 3 years ago

mrumi commented 3 years ago

Hello I have run the command to convert fasta sequences to TFRecord as instructed. Here's my command ./tfrec_train_kmer.sh -i SRR1777715.fasta -v tokens_merged_12mers.txt -o SRR1777715.tfrec -s 20480000 -k 12

This is my output parallel successfully detected... ERROR : seq-shuf not detected seq-shuf exists in bin folder. Not sure why this error is occurring. Can you please suggest a solution?

MicrobeLab commented 3 years ago

Did you add seq-shuf to your path? export PATH=/path/to/DeepMicrobes/bin:$PATH

If seq-shuf still fails, try installing the seq-scripts following the manual in https://github.com/thackl/seq-scripts