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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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nanocompore sampcomp - Reading eventalign index files - References found in index: 0 #152

Closed ADelgadoT closed 3 years ago

ADelgadoT commented 3 years ago

Hi,

I'm trying to run nanocompore on a set of samples using this command: nanocompore sampcomp --nthreads 8 --file_list1 sample_1/out_eventalign_collapse.tsv --file_list2 sample_2/out_eventalign_collapse.tsv --label1 sample_1 --label2 sample_2 --fasta rRNA_Maternal.fa --outpath ./sample_1--sample_2_nanocompres/ --sequence_context 4 --downsample_high_coverage 10000 --pvalue_thr 1 --logit --comparison_methods GMM,KS,MW,TT --overwrite

When running it, I get the following error: 

Initialising SampComp and checking options
Only 1 replicate found for condition CK-43-TOT-WT2
This is not recommended. The statistics will be calculated with the logit method
Only 1 replicate found for condition CK-44-TOT-WT4
This is not recommended. The statistics will be calculated with the logit method
Initialising Whitelist and checking options
Reading eventalign index files
    References found in index: 0
Filtering out references with low coverage
    References remaining after reference coverage filtering: 0
Starting data processing
0 Processed References [00:00, ? Processed References/s]
Loading SampCompDB
Traceback (most recent call last):
  File "/usr/local/python/versions/3.6.3/bin/nanocompore", line 8, in <module>
    sys.exit(main())
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanocompore/__main__.py", line 139, in main
    args.func(args)
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanocompore/__main__.py", line 174, in sampcomp_main
    db = s()
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanocompore/SampComp.py", line 268, in __call__
    log_level=self.__log_level)
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanocompore/SampCompDB.py", line 82, in __init__
    raise NanocomporeError("The result database is empty")
nanocompore.common.NanocomporeError: The result database is empty

Do you have any idea about how to solve it? I've been looking through your documentation and I could not fix it.

Thanks in advance for the help!

tleonardi commented 3 years ago

Hi @ADelgadoT, the issue is explained in these line:

Reading eventalign index files
    References found in index: 0
Filtering out references with low coverage
    References remaining after reference coverage filtering: 0

For some reasons it looks like your input is actually empty. Could you check the output file of NanopolishComp? What do they contain?