AlexanderDilthey
commented
5 years ago Hi,
Hmm, this is weird - it seems the program can’t open the main output file. My initial guess was file system/permission issues, but given that the .1 file was created, this seems unlikely. Have you tried writing into another directory? All basic sanity checks, like space on disk, ok?
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From: aroelo notifications@github.com Sent: Wednesday, January 30, 2019 08:47 To: DiltheyLab/MetaMaps Cc: Subscribed Subject: [DiltheyLab/MetaMaps] Assertion 'combinedOutput.is_open()' failed (#11)
Hi Alexander,
I just ran into an issue when using mapDirectly with my custom database.
The last lines of output are:
Added C3600|kraken:taxid|185218|NC_012519.1 with length 7781; est. memory ~24.2109 GB Added C5076|kraken:taxid|389469|NC_008717.1 with length 36415; est. memory ~24.2112 GB Added C4950|kraken:taxid|673515|NC_021069.1 with length 10865; est. memory ~24.2113 GB Added C959|kraken:taxid|170617|NC_005038.1 with length 99657; est. memory ~24.2123 GB Added C4768|kraken:taxid|1746063|NC_028391.1 with length 1940; est. memory ~24.2123 GB Added C5424|kraken:taxid|1688637|NC_027706.1 with length 9829; est. memory ~24.2124 GB Added C2200|kraken:taxid|10815|NC_001928.2 with length 2632; est. memory ~24.2125 GB Added kraken:taxid|4232|C1004|NW_019010654.1 with length 9845; est. memory ~24.2125 GB Added C2630|kraken:taxid|223307|NC_002049.1 with length 2542; est. memory ~24.2126 GB Added C5772|kraken:taxid|71186|NC_009605.1 with length 2562; est. memory ~24.2126 GB Added C640|kraken:taxid|201862|NC_007216.1 with length 9695; est. memory ~24.2127 GB
Call storeCurrentState with 7338
INFO, skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 70758415) ... (242454, 1) INFO, skch::Sketch::computeFreqHist, With threshold 0.001%, ignore minimizers occurring >= 7400 times during lookup. INFO, skch::Map::mapQuery, [count of mapped reads, reads qualified for mapping, total input reads] = [160689, 401370, 1705578] INFO, skch::Map::Map, Time spent mapping the query : 492.806 sec INFO, skch::Sketch::build, minimizers picked from reference = 685249698
Index construction DONE, wrote 1 files.
metamaps: src/map/mapWrap.h:40: void mapWrap::unifyFiles(std::cxx11::string, const skch::Parameters&, std::vector<std::cxx11::basic_string
After running the following command:
/usr/bin/time -v /opt/MetaMaps-master/metamaps mapDirectly -t 20 --all -r ./myDB/DB.fa -q /datadrivehdd1/nanopore/03_projects/campanula/reads/campanula_PCS108_a2.3.0.fastq -o ./classification_results --maxmemory 100 &> output.txt
I have added the corresponding output.txt file if you would like to see the full output. output.txthttps://github.com/DiltheyLab/MetaMaps/files/2808267/output.txt
Only a 'classification_results.1' file is created, and as I read earlier this means that classify didn't finish completely.
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aroelo
xlinxlin
Command is: 
Here is the output for 
Hi Alexander,
I just ran into an issue when using mapDirectly with my custom database.
The last lines of output are:
After running the following command:
/usr/bin/time -v /opt/MetaMaps-master/metamaps mapDirectly -t 20 --all -r ./myDB/DB.fa -q /datadrivehdd1/nanopore/03_projects/campanula/reads/campanula_PCS108_a2.3.0.fastq -o ./classification_results --maxmemory 100 &> output.txtI have added the corresponding output.txt file if you would like to see the full output. output.txt
Only a 'classification_results.1' file is created, and as I read earlier this means that classify didn't finish completely.