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Neither --stdin nor --infile specified: assuming input from stdin. Warning: --cutoff is set to 0, output will be *huge* Either --pfmfile or --cutoff is missing - aborting! Use --help to get help--seqfile is missing - aborting! Use --help to get helpChromosome Coordinate Sequence Score Strand Base strand 8@@@P@@x@@@h@P@p@main?& .>COTRASIF version %0.2f A C G T %0.3fInterposition %d: %c %dhmmfinderpwmfinderHMMPWMERROR: %s. Unexpected end of fileutils.cinput->pfm_height == 4input->pfm_width < 5000input->pfm_width < 1250 PFM: Calculated PWM: (c) B. Tokovenko (2006-2011) and R. Golda (2008-2009). Portions (c) O. Protas (2009). Use COTRASIF online at http://biomed.org.ua/COTRASIF/ If you use COTRASIF in your research, please cite: Bogdan Tokovenko, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya, and Anna El'skaya. COTRASIF: conservation-aided transcription-factor-binding site finder. Nucleic Acids Research, 2009, Vol. 37, No. 7, e49. DOI 10.1093/nar/gkp084. http://nar.oxfordjournals.org/cgi/content/abstract/gkp084v1 Minimal model score (normalized) = %f (%f) Maximal model score (normalized) = %f (%f) This shouldn't generally happen, but window_raw_score is 0! *** Critical error ***: strpos() failed to find %c in %s! Sequences are shorter than 7 symbols - aborting *** Warning ***: input FASTA line length is longer than %i and will result in unpredicted behaviour! PFM matrix is shorter than 7 symbols - aborting. Notice: PFM is shorter than 7 symbols. Number of matrix elements: %u Detected matrix width (TFBS length): %u Text read from pfmfile (%u bytes): %s Text read from seqfile (%u bytes): %s get_pfm)\(???@@@9B.?@_@@E_libcotrasif.c*** Critical, exiting. %iScore is 0! %s %u %f %i %i Scores of input sequences: %s %f input->pfm != ((void *)0)In dnabase2index (%s:%i) n is %i for base '%c' *** Warning ***: non-Ensembl FASTA header found! *** Setting sequence strand to '1'. *** Only the sequence identifier from FASTA header will be used. *** This warning is displayed only once, no matter how many more non-Ensembl headers are found later. *** Failed to compile regex: %s *** Failed to find sequence identifier in this header: %s *** Please use only [a-zA-Z0-9_-] characters for identifiers. *** Assigning this randomly generated identifier: %s This should have never happened. Corrected minimal model score (normalized) = %f (%f) Corrected maximal model score (normalized) = %f (%f) Initial cut-off: raw %f, normalized %f; un-normalized 0.01 decrement: %f. ??@@@@@ @@0@|@@E@g@f@@a#@;'@;+@fw/@Sf3@D7@ <@1MA@@` D@p&ů.I@CbN@ JR@X$̦W@.?\@8KnI`@(<=42e@hhpc?j@ qUho@ qUht@* y@~@recalculate_matrix@Y@{Gz?п?@? #<;h, \ܤTlܨ,L,|L \LLl|| @N@^@n@~@@@@@@@@@@@.@>@N@^@n@~@@@@@@@@@@@.@>@N@^@n@~@@@@@@h@h@h@h@h@h@h@i@ i@i@i@ACGTNGCC: (Debian 4.4.5-8) 4.4.5GCC: (Debian 4.4.5-10) 4.4.5.shstrtab.interp.note.ABI-tag.note.gnu.build-id.gnu.hash.dynsym.dynstr.gnu.version.gnu.version_r.rela.dyn.rela.plt.init.text.fini.rodata.eh_frame_hdr.eh_frame.ctors.dtors.jcr.dynamic.got.got.plt.data.bss.comment @@ !<@<$8`@`x4o@<> @(F@ @@ No @ n[ox @x `j @ t @ P ~@y@@(Th@h h@ h 4|@4|l}@}````h`hp`p` `@09