medaka consensus error

[tarah28]

Hello! Hoping you can please help with this. I am just running the test data but can't figure out how to get medaka consensus working for the pipeline, can you please help? Thanks so much.

We are unable to use docker here so need to use conda.

COMMAND: nextflow run main.nf -profile test,conda

[d5/b19fa4] process > QC (1) [100%] 1 of 1 ✔ [00/bba3f0] process > fastqc (1) [100%] 1 of 1 ✔ [47/ef83da] process > kmer_freqs (1) [100%] 1 of 1 ✔ [60/c14484] process > read_clustering (1) [100%] 1 of 1 ✔ [61/562b4b] process > split_by_cluster (1) [100%] 1 of 1 ✔ [bc/107089] process > read_correction (1) [100%] 8 of 8 ✔ [d2/17da57] process > draft_selection (6) [ 75%] 6 of 8 [c4/6c6240] process > racon_pass (6) [100%] 6 of 6 [24/5ee26e] process > medaka_pass (1) [ 16%] 1 of 6, failed: 1 [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [97/496983] process > output_documentation [100%] 1 of 1 ✔ WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 2 failed due to not enough overlaps. Taking draft read as consensus WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 5 failed due to not enough overlaps. Taking draft read as consensus WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 1 failed due to not enough overlaps. Taking draft read as consensus WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 4 failed due to not enough overlaps. Taking draft read as consensus WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 7 failed due to not enough overlaps. Taking draft read as consensus WARN: Sample mock4_run3bc08_5000 : Racon correction for cluster 6 failed due to not enough overlaps. Taking draft read as consensus Error executing process > 'medaka_pass (1)'

Caused by: Process medaka_pass (1) terminated with an error exit status (1)

Command executed:

if medaka_consensus -i corrected_reads.correctedReads.fasta -d racon_consensus.fasta -o consensus_medaka.fasta -t 4 -m r941_min_hi gh_g303 ; then echo "Command succeeded" else cat racon_consensus.fasta > consensus_medaka.fasta fi

Command exit status: 1

Command output: Checking program versions This is medaka 1.2.2 Program Version Required Pass bcftools 1.11 1.9 True bgzip 1.11 1.9 True minimap2 2.17 2.11 True samtools 1.11 1.9 True tabix 1.11 1.9 True Aligning basecalls to draft Removing previous index file /home/tlynch/programs/NanoCLUST/work/5d/a447253a90b3dad02af6df1295581a/racon_consensus.fasta.mmi Removing previous index file /home/tlynch/programs/NanoCLUST/work/5d/a447253a90b3dad02af6df1295581a/racon_consensus.fasta.fai Running medaka consensus Failed to run medaka consensus.

Command error: File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/sequential.py", line 208, in add layer(x) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/wrappers.py", line 5 39, in call return super(Bidirectional, self).call(inputs, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 952, in call input_list) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 1091, in _functional_construction_call inputs, input_masks, args, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 822, in _keras_tensor_symbolic_call return self._infer_output_signature(inputs, args, kwargs, input_masks) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 863, in _infer_output_signature outputs = call_fn(inputs, *args, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/wrappers.py", line 6 53, in call initial_state=forward_state, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 660, in call return super(RNN, self).call(inputs, *kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/engine/base_layer.py", line 1012, in call outputs = call_fn(inputs, args, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent_v2.py", li ne 439, in call inputs, initialstate, = self._process_inputs(inputs, initial_state, None) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 859, in _process_inputs initial_state = self.get_initial_state(inputs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 643, in get_initial_state inputs=None, batch_size=batch_size, dtype=dtype) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 1948, in get_initial_state return _generate_zero_filled_state_for_cell(self, inputs, batch_size, dtype) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 2987, in _generate_zero_filled_state_for_cell return _generate_zero_filled_state(batch_size, cell.state_size, dtype) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 3005, in _generate_zero_filled_state return create_zeros(state_size) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/keras/layers/recurrent.py", line 3000, in create_zeros return array_ops.zeros(init_state_size, dtype=dtype) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/util/dispatch.py", line 201, in w rapper return target(*args, *kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 2819, in wrapped tensor = fun(args, kwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 2868, in zeros output = _constant_if_small(zero, shape, dtype, name) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 2804, in _constant_if_small if np.prod(shape) < 1000: File "<__array_function__ internals>", line 6, in prod File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 3052, in prod keepdims=keepdims, initial=initial, where=where) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduct ion return ufunc.reduce(obj, axis, dtype, out, passkwargs) File "/home/tlynch/miniconda3/envs/nextflow22.10/lib/python3.7/site-packages/tensorflow/python/framework/ops.py", line 855, in _ _array__ " a NumPy call, which is not supported".format(self.name)) NotImplementedError: Cannot convert a symbolic Tensor (bidirectional/forward_gru1/strided_slice:0) to a numpy array. This error ma y indicate that you're trying to pass a Tensor to a NumPy call, which is not supported Failed to run medaka consensus. .command.sh: line 5: consensus_medaka.fasta: Is a directory

Work dir: /home/tlynch/programs/NanoCLUST/work/24/5ee26e068dad1554269abe4696aeb7

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

[nf-core/nanoclust] Pipeline completed with errors WARN: Killing running tasks (3)

[SieglindeCoppens]

Hi!

I ran into the same issue and fixed it by changing a line in main.nf. I changed line 408: cat $draft > consensus_medaka.fasta To: cat $draft > consensus_medaka.fasta/consensus.fasta Otherwise, it ran into issues when medaka consensus failed. I hope this works for you as well!