DiltheyLab / MetaMaps

Long-read metagenomic analysis
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Assertion 'combinedOutput.is_open()' problem? when executing mapDirectly #80

Closed pehenrique closed 1 month ago

pehenrique commented 1 month ago

I have a set of 29 fastq files and for 28 of them I manage to run metamaps without problem. For one of them I keep receiving the same error during mapDirectly step and I could not figure it out what is the cause of this. The same error was reported before here https://github.com/DiltheyLab/MetaMaps/issues/11 but it was not clear for me what was done to solve it. This is the command line used:

metamaps mapDirectly --all --pi 95 -w 100 -m '200' -r '/Databases/ViralRefseq/DB.fa' -q 8_FP_T1.fastq.gz -o 8_FP_T1_classification_results --maxmemory 12

And this is the output:

Command output:
  >>>>>>>>>>>>>>>>>>
  Reference = [/Databases/ViralRefseq/DB.fa]
  Query = [8_FP_T1.fastq.gz]
  Kmer size = 16
  Window size = 100
  Min. read length >= 200
  Alphabet = DNA
  P-value = 0.0373189
  Percentage identity threshold = 95
  Report all = 1
  Target max. memory = 12884901888
  Threads = 1
  Mapping output file = 8_FP_T1_classification_results
  >>>>>>>>>>>>>>>>>>
  Parameters used:
        - alphabetSize: 4
        - kmerSize: 16
        - minReadLength: 200
        - p_value: 0.0373189
        - percentageIdentity: 95
        - windowSize: 100
        - maximumMemory: ~12 GB

 Added C1369|kraken:taxid|x433|NC_063383.1 with length 197209; est. memory ~0.000253149 GB
 Added C8272|kraken:taxid|x432|NC_003310.1 with length 196858; est. memory ~0.000383971 GB

  Call storeCurrentState with 2

  INFO, skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 1002) ... (16, 1)
  INFO, skch::Sketch::computeFreqHist, With threshold 0.001%, consider all minimizers during lookup.
  INFO, skch::Map::mapQuery, [count of mapped reads, reads qualified for mapping, total input reads] = [168035, 185053, 185053]
  INFO, skch::Map::Map, Time spent mapping the query : 14.2884 sec
  INFO, skch::Sketch::build, minimizers picked from reference = 7860

  Index construction DONE, wrote 1 files.

After executing metamaps, 3 files are created: image

As suggested in the case mentioned above, I did the same and executed echo 1 > classification_results and ls -l classification_results and this is the results: -rw-r--r-- 1 domain users 2 Jul 23 13:54 classification_results

Thank you in advance, any suggestions or comments will be highly appreciated.