search

ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
368 stars 66 forks source link

Output is still empty after two days running #52

Closed rainjy closed 4 years ago

rainjy commented 5 years ago

command: fastANI --ql xx --rl xx -t 23 --matrix -o fastANI.out

But Only a log as follow, and never update

Reference = [total 1125 fasta seq] Query = [total 5000 fasta seq] Kmer size = 16 Fragment length = 3000 Threads = 23 ANI output file = fastANI.out

INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 44870461 INFO [thread 0], skch::Sketch::index, unique minimizers = 32929725 INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 25158025) ... (434, 1) INFO [thread 0], skch::Sketch::computeFreqHist, With threshold 0.001%, ignore minimizers occurring >= 43 times during lookup. INFO [thread 0], skch::main, Time spent sketching the reference : 147.643 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.802434 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000257816 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #2 : 2.47368 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000986272 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #3 : 1.4448 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000543327 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #4 : 1.10718 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000373789 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #5 : 1.60302 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000503294 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #6 : 1.01921 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000374961 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #7 : 0.698442 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000139954 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #8 : 1.16008 sec INFO [thread 0], skch::main, Time spent post mapping : 0.00037629 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #9 : 1.949 sec INFO [thread 0], skch::main, Time spent post mapping : 0.000728267 sec INFO [thread 0], skch::main, Time spent mapping fragments in query #10 : 0.912171 sec ......

Ovv3 commented 5 years ago

I have virtually the same result, or very similar one... Look! The only [thread 0] is working, but not 0-22 ones expected. What a reason?

cjain7 commented 5 years ago

Perhaps try i) building code from source using recent C++ compilers or ii) try running code on alternative servers. Also, multi-threading is only effective when you have multiple cores available and free.

rainjy commented 5 years ago

@cjain7 maybe, I will try it

cjain7 commented 4 years ago

Assuming this is resolved. Please create a new issue if not.