sarahjeeeze
commented
1 year ago Hi, sorry for the late reply. Pre-concatenating would not impact the output results, this workflow has since been updated so may be worth trying the latest version. Let us know if you still have any issues.
Hi, I just wanted to bring up an issue that I have run into when using the wf-bacterial-genomes workflow. I am getting this error on the medakaNetwork process when I run the workflow on a directory of fastqs from one barcode. However, if I pre concatenate the barcode fastqs I do not run into this issue. For the time being is pre concatenating a suitable fix, would it harm the final output of the analysis?
Thank you.
` Error executing process > 'calling_pipeline:medakaNetwork (2)'
Caused by: Process
calling_pipeline:medakaNetwork (2)terminated with an error exit status (137)Command executed:
medaka consensus 00-480.reads2ref.bam 00-480.2.consensus_probs.hdf --threads 2 --model r941_prom_variant_g360 --region "contig_2:0-1000000 "
Command exit status: 137
Command output: (empty)
Command error: /home/epi2melabs/conda/lib/python3.8/site-packages/tensorflow/python/ops/random_ops.py:285: SyntaxWarning: "is" with a literal. Did you mean "=="? minval_is_zero = minval is 0 # pylint: disable=literal-comparison /home/epi2melabs/conda/lib/python3.8/site-packages/tensorflow/python/ops/random_ops.py:286: SyntaxWarning: "is" with a literal. Did you mean "=="? maxval_is_one = maxval is 1 # pylint: disable=literal-comparison /home/epi2melabs/conda/lib/python3.8/site-packages/tensorflow/python/ops/ragged/ragged_batch_gather_with_default_op.py:84: SyntaxWarning: "is not" with a literal. Did you mean "!="? if (default_value.shape.ndims is not 0 /home/epi2melabs/conda/lib/python3.8/site-packages/tensorflow/python/ops/ragged/ragged_batch_gather_with_default_op.py:85: SyntaxWarning: "is not" with a literal. Did you mean "!="? and default_value.shape.ndims is not 1): [17:13:51 - Predict] Setting tensorflow inter/intra-op threads to 2/1. [17:13:51 - Predict] Processing region(s): contig_2:0-1000000 [17:13:51 - Predict] Using model: /home/epi2melabs/conda/lib/python3.8/site-packages/medaka/data/r941_prom_variant_g360_model.hdf5. [17:13:51 - Predict] Processing 1 long region(s) with batching. [17:13:51 - MdlStore] filepath /home/epi2melabs/conda/lib/python3.8/site-packages/medaka/data/r941_prom_variant_g360_model.hdf5 [17:13:52 - Sampler] Initializing sampler for consensus of region contig_2:0-1000000. [17:13:52 - PWorker] Running inference for 1.0M draft bases. [17:14:00 - Feature] Processed contig_2:0.0-999999.2 (median depth 173.0) [17:14:00 - Sampler] Took 8.76s to make features. [17:14:22 - PWorker] Batches in cache: 3. [17:14:22 - PWorker] 34.1% Done (0.3/1.0 Mbases) in 30.8s .command.sh: line 3: 29 Killed medaka consensus 00-480.reads2ref.bam 00-480.2.consensus_probs.hdf --threads 2 --model r941_prom_variant_g360 --region "contig_2:0-1000000 " `