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nanoporetech / medaka

Sequence correction provided by ONT Research
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Medaka_consensus: Could not retrieve index file for 'calls_to_draft.bam' #467

Closed wn835166087 closed 7 months ago

wn835166087 commented 7 months ago

Describe the bug I'm using medaka_consensus for sequence polish, here is my command docker1 run -u root --rm -v /workdir/$USER/mydata/:/data -w /data --gpus all ontresearch/medaka:latest medaka_consensus -i ${BASECALLS} -d ${DRAFT} -o ${OUTDIR} -m r941_min_sup_g507 And I got euro [E::idx_find_and_load] Could not retrieve index file for 'calls_to_draft.bam' Failed to read .bam file 'calls_to_draft.bam'.Failed to run medaka consensus.

Logging Please attach any relevant logging messages. (Use ``` before and after code blocks).

TF_CPP_MIN_LOG_LEVEL is set to '3'
Cannot import pyabpoa, some features may not be available.
Cannot import pyabpoa, some features may not be available.
Cannot import pyabpoa, some features may not be available.
Checking program versions
This is medaka 1.10.0
Cannot import pyabpoa, some features may not be available.
Program    Version    Required   Pass     
bcftools   1.18       1.11       True     
bgzip      1.18       1.11       True     
minimap2   2.26       2.11       True     
samtools   1.18       1.11       True     
tabix      1.18       1.11       True     
Warning: Output medaka1_R9_CN already exists, may use old results.
Cannot import pyabpoa, some features may not be available.
[16:11:05 - MdlStrTF] Successfully removed temporary files from /tmp/tmp41p3l__e.
Cannot import pyabpoa, some features may not be available.
[16:11:05 - MdlStrTF] Successfully removed temporary files from /tmp/tmp7bm5h4lc.
Not aligning basecalls to draft, calls_to_draft.bam exists.
Running medaka consensus
Cannot import pyabpoa, some features may not be available.
[16:11:11 - Predict] Setting tensorflow inter/intra-op threads to 1/1.
[16:11:11 - Predict] Processing region(s): contig_1:0-10143 contig_100:0-339 contig_1000:0-14474 contig_1001:0-5628 contig_1002:0-2095 contig_1003:0-36638 contig_1004:0-5461 contig_1005:0-17854 contig_1007:0-1178 contig_1008:0-1768 contig_1009:0-22981 contig_1010:0-14924 contig_1011:0-20152 contig_1012:0-3862 contig_1013:0-28330 contig_1014:0-6531 
[16:11:11 - Predict] Using model: /home/epi2melabs/conda/lib/python3.8/site-packages/medaka/data/r941_min_sup_g507_model.tar.gz.
[16:11:12 - Predict] Found a GPU.
[16:11:12 - Predict] If cuDNN errors are observed, try setting the environment variable `TF_FORCE_GPU_ALLOW_GROWTH=true`. To explicitely disable use of cuDNN use the commandline option `--disable_cudnn. If OOM (out of memory) errors are found please reduce batch size.
[16:11:12 - BAMFile] Creating pool of 16 BAM file sets.
[E::idx_find_and_load] Could not retrieve index file for 'calls_to_draft.bam'
Failed to read .bam file 'calls_to_draft.bam'.Failed to run medaka consensus.

Environment (if you do not have a GPU, write No GPU):

Additional context Add any other context about the problem here.

cjw85 commented 7 months ago

From your logs it appears that you have rerun the program with the output directory pointing to an existing output folder. The program has detected these partial outputs and so skipped several steps. I would need to see the output from the previous run to understand why the bam index was not present.

cjw85 commented 7 months ago

Closing due to lack of response.