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:
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:
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.
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:
After executing metamaps, 3 files are created:
As suggested in the case mentioned above, I did the same and executed
echo 1 > classification_results
andls -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.