meren
commented
9 years ago This morning I got this same message from 3 different sources: as an e-mail, as a comment to the oligotyping page, and as a bug report. There is a Google Groups for these questions linked from the oligotyping project page:
https://groups.google.com/forum/#!forum/oligotyping
Please ask your question there.
I finally arrived to oligotyping command, and obtain the following (several results files, but no figures..and I need the entropy figures for each oligotype to choose the positions for the second run. So I am stopped at this point. Please help me :
Output directory .................................................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10 Temporary files directory ........................................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/TMP Extraction info output file ......................................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/RUNINFO Quality scores were provided .....................................: False Command line .....................................................: /usr/bin/oligotype TOTLplantlimp_aligned_pfilteredMEGA.fasta TOTLplantlimp_aligned_pfilteredMEGA.fasta-ENTROPY -c1 -M10 --gen-html Number of sequences analyzed .....................................: 6,818 Number of characters in each alignment ...........................: 496 Number of entropy components to be selected automatically ........: 1 Number of entropy components chosen by the user ..................: 0 Oligotype sets were requested to be generated ....................: False Skip performing basic analyses ...................................: False Min number of samples oligotype expected to appear ...............: 1 Min % abundance of oligotype in at least one sample ..............: 0.0 Min total abundance of oligotype in all samples ..................: 0 Min substantive abundance of an oligotype (-M) ...................: 10 Base locations of interest in the alignment ......................: 1 Number of samples found ..........................................: 7
Number of unique oligotypes (raw) ................................: 4
Oligotypes after "min number of samples" elimination .............: 4
Oligotypes after "min % abundance in a sample" elimination .......: 4
Oligotypes after "min total abundance (-A)" elimination ..........: 4
Oligotypes after "min substantive abundance (-M)" elimination ....: 2
Number of sequences represented after quality filtering ..........: 6,803
Random colors for oligotypes .....................................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/COLORS FASTA file for abundant oligotypes ...............................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/OLIGOS.fasta NEXUS file for abundant oligotypes ...............................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/OLIGOS.nexus Environment file .................................................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/ENVIRONMENT.txt Sample/oligotype abundance data matrix (counts) ..................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/MATRIX-COUNT.txt Sample/oligotype abundance data matrix (percents) ................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/MATRIX-PERCENT.txt Read distribution among samples table ............................: /home/oligotyping/TOTLplantlimp_aligned_pfilteredMEGA-c1-s1-a0.0-A0-M10/READ-DISTRIBUTION.txt [24 Jul 15 13:00:37 Generating Entropy Figures] 0 of 2 done in 0 threads ( (...)