DeepMicrobes

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Error in tfrec_train_kmer.sh with SILVA 138.1 SSU database as training set

5

Hi, I would like to train the network with SILVA 138.1 SSU database using `tfrec_train_kmer.sh -i SILVA_138.1_SSURef_NR99_tax_silva.fasta -v /vocabulary/tokens_merged_12mers.txt -o train.tfrec -s 20480000 -k 12 ` However, i am getting...

oschakoory

Error in tfrec_train_kmer.sh with a customized training set

3

Hi, I'm trying to use `tfrec_train_kmer.sh` for a training dataset I constructed, and I'm struggling with this. I got the errors below. ``` (DeepMicrobes) root@bbf7145cde62:/workspace/vamb-data/airways# tfrec_train_kmer.sh -i dmtrain.fa -v /workspace/czj/tokens_merged_12mers.txt...

shawnnn3di

failed prediction only in some samples

2

I'm using a docker container with TF1.15 to run DeepMicrobes. I know it might not have been tested using TF1.15 but that is the compatible one with my platform. It...

ramtinz

running DeepMicrobes in RHEL 8.4

5

Hi I cannot run the example prediction task on a server with red hat 8.4 as OS. When I run it I get this error: E tensorflow/stream_executor/cuda/cuda_blas.cc:647] failed to run...

ramtinz

problem running the example tfrec conversion on Windows Subsystem for Linux WSL and likewise on docker

7

Hi, I installed DeepMicrobes following the provided [guide ](https://github.com/MicrobeLab/DeepMicrobes/blob/master/document/install.md) but did not have any success at running the tfrec_predict_kmer for the provided example file. Is there any solution to this?...

ramtinz

Hello, This isn't a real issue. Just wondering what kind of continued improvements or new releases to expect (beyond support), given most of the new commits to this project stopped...

dbrami

Error: seq-shuf not detected

1

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...

mrumi

ERROR :parallel not detected.

3

run command: (pip-tensorflow) (DeepMicrobes) [xxxx@compute40 DeepMicrobes]$ tfrec_predict_kmer.sh -f ../test/SRR5935743_clean_1.fastq -r ../test/SRR5935743_clean_2.fastq -t fastq -v ../vocab/tokens_merged_12mers.txt -o srr -s 4000000 -k 12 return : ERROR : parallel not detected Help me.

chulghim

Different prediction results for the same fastq files

2

Hi Qiaoxing, I used DeepMicrobes for species prediction in a system with GPU and a system without GPU (only CPUs). Surprisingly, predicted species are different for the same fastq samples....

ramtinz

reloading model resets accuracy

1

Hi, I'm trying to run DeepMicrobes on my own data but I'm running into some trouble. When I train seq2species through DeepMicrobes, everything seems to be working fine and training...

cvdelannoy